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History of changes, improvements and new features

March 21, 2003

New cross-references have been introduced in Swiss-Prot:

• Explicit links to GeneDb_SPombe, the Schizosaccharomyces pombe GeneDB, example: O94534.
• Implicit links to CleanEx, a gateway to public gene expression data via officially approved gene names, example: P02751.

There is a new Swiss-Prot document, arath.txt - Index of Arabidopsis thaliana entries and their corresponding gene designations.

An interface to PRATT has been implemented on ExPASy. PRATT is a tool to discover patterns that are conserved in a set of protein sequences. The patterns are reported using the PROSITE format. The ExPASy BLAST result representation has been modified to allow direct submission of a number of sequences to PRATT.

The ExPASy BLAST interface now allows to perform tblastn searches against individual microbial genomes (EMBL genome records, including plasmids).

Throughout the ExPASy server, the navigation bar at the top of every page now includes a search bar, for quick access to Swiss-Prot, TrEMBL, PROSITE, SWISS-2DPAGE, ENZYME, Taxonomy, HAMAP and ExPASy site search.

November 19, 2002

We are happy to announce a new ExPASy mirror site in Bolivia, http://bo.expasy.org, hosted by the Universidad Católica Boliviana in Cochabamba.

October 25, 2002

ExPASyBar, a very useful navigation bar to the most important databases and tools on the ExPASy server, has been developed by Martin Hassman, with input from the ExPASy team. ExPASyBar is an add-on to the Mozilla web browser (i.e. it does not work with Netscape, MS Internet Explorer and other browsers). Installation is very simple. ExPASyBar can be configured to use the ExPASy mirror of the user's choice (in the Edit/Preferences/Advanced/ExPASyBar menu of Mozilla).

August 27, 2002

The last "What's new on ExPASy" is more than a year old, which means that some of the changes and "new" features and services are not all that new anymore.... We are trying to list here the most important changes, and we will try to report new tools and documents again more frequently in the future!

=== ExPASy ===

• We are happy to announce that since the beginning of the year 2002, there is an ExPASy mirror site in the USA, http://us.expasy.org, hosted by the North Carolina Supercomputing Center (NCSC). Some users may have noticed upon their connection to www.expasy.org, that they are redirected to a mirror site that is closer to their geographic location, or that is less heavily loaded. If you feel that you are redirected to a mirror site for which the network connection is slow, please let us know.
• News on the FTP server:
  1. PROSITE updated data and documentation files are now made available via FTP even between releases, in the directory /databases/prosite/release_with_updates/. This data always corresponds to the version of the database available for web access via the PROSITE page.
  2. Up-to-date plain-text versions of all SWISS-PROT documents can be downloaded by ftp, in the directory /databases/swiss-prot/updated_doc/.
  3. Three "special selections" have been added:
     • merops.seq - all SWISS-PROT entries cross-referenced to the MEROPS database
     • mitoch.seq - Mitochondrion encoded proteins (entries with "Mitochondrion" on OG lines)
     • plastid.seq - Chloroplast and cyanelle encoded proteins (entries with "Chloroplast" or "Cyanelle" on OG lines)

=== TOOLS ===

Two tools have been added to our collection of sequence analysis and proteomics tools:

• The Sulfinator predicts tyrosine sulfation sites in protein sequences, based on Hidden Markov Models.
• PeptideCutter predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. It displays the query sequence with the possible cleavage sites mapped on it, as well as a table of cleavage site positions.

Major updates have been performed on two tools:

• The ScanProsite interface has been remodeled, with more options and databases, and a graphical view of the results. A standalone program, ps_scan is now available.
• The BLAST interface now allows searches in PDB. The output page displays hits found with Pfam HMMs and PROSITE profiles on the query sequence.

=== SWISS-PROT ===

• New cross-references have been introduced to various databases: AraC-XylS, Genew, Gramene, several 2D-PAGE databases, Ensembl, GeneLynx, ListiList, ModBase, PhosSite, ProtoNet, Source and TIGRFAMs.
  The List of databases cross-referenced in SWISS-PROT contains, for each database, a short description, the link type (explicit or implicit), and the server URL. In the case of explicit links, you can click on the word "Explicit" (example: Genew) to retrieve a list of all SWISS-PROT entries linked to the corresponding database.
  The cross-references to the following databases have been deleted, because the databases are either no longer available on the WWW, or because they have become commercial even for academic users: CarbBank, DOMO, GCRDb, Mendel, YEPD and YPD.

• The NiceProt view of SWISS-PROT has been further improved: access to documentation has been facilitated by adding "mouse-over" hypertext links from various sections in NiceProt to the corresponding information in the user manual. Those hypertext links, which give access to documentation rather than the data related to the protein entry, are visually different from the ordinary hyperlinks. While they are not immediately recognizable as such, the user can see that they are clickable by moving the mouse pointer over the section headings such as "References" or "Keywords". A short description of the linked information appears at the bottom of the web browser, and when clicked, a small additional window is opened with related information extracted from the user manual.

  Similarly, in the "Cross-references" section, the names of the databases to which an entry is cross-referenced are linked to the corresponding sections in the document dbxref.txt (List of databases cross-referenced in SWISS-PROT).

• Three SWISS-PROT documents have been released since the last announcement:
  • bucai.txt - Index of Buchnera aphidicola (subsp. Acyrthosiphon pisum) entries
  • mycpn.txt - Index of Mycoplasma pneumoniae strain M129 entries
  • plasmid.txt - List of plasmids

• The Human proteomics initiative (HPI) status report page has been remodeled and now contains more detailed information about the status of annotation of human SWISS-PROT entries.
• The HAMAP project aims to annotate semi-automatically complete bacterial and archaeal proteomes up to the quality standards of SWISS-PROT. Several proteomes have already been completed and are continuously updated. Up-to-date statistics are available on the HAMAP status page
• Note that upcoming format changes in the next SWISS-PROT release are always described in the release notes for the current release.
• Although not hosted physically on the ExPASy server, the NEWT Taxonomy browser is provided and maintained by members of the SWISS-PROT group, and serves as an entry point into SWISS-PROT and TrEMBL using taxonomic search criteria.

=== SWISS-2DPAGE ===

New cross-references, reference maps, and a document have been added:

• Cross-references to recent fully federated 2-DE databases, built with the Make2ddb package, are provided. These are now COMPLUYEAST-2DPAGE, PHCI-2DPAGE, PMMA-2DPAGE, and Siena-2DPAGE. The list of links is updated each time a SWISS-2DPAGE release is completed.
• SDS-PAGE and 2-D PAGE of nucleolar proteins from Human HeLa cells have been added to the list of reference maps . These masters are named respectively NUCLEOLI_HELA_1D_HUMAN and NUCLEOLI_HELA_2D_HUMAN.
• A FAQ (Frequently Asked Questions) has been provided. We hope you will find answers to most of your questions in this new document.

June 30, 2001

New cross-references have been added from relevant SWISS-PROT entries to three databases:

• SMART - Protein domain database (example: O43707).
• Leproma - Database dedicated to the analysis of the genome of the leprosy bacillus Mycobacterium leprae (example: Q9CBW4).
• MypuList - Mycoplasma pulmonis genome database (example: P58174).

The keyword "Complete proteome" has been introduced to all SWISS-PROT/TrEMBL entries describing a protein which is thought to be expressed by an organism whose genome has been completely sequenced. This keyword is so far only used for microbial (bacterial and archaeal) proteins. A complete set of proteins from a microbial genome can therefore be obtained using this keyword across SWISS-PROT and TrEMBL.

A new and improved version of the NiceProt view of SWISS-PROT is available (example). Some of its new features are:

• It provides a link to a printer-friendly view of a SWISS-PROT entry.
• It displays the length of certain features in the FT lines.
• It provides access to a new tool, the 'Feature aligner' which allows to select features for submission to the ClustalW multiple alignment program.

SWISS-PROT release statistics are now available for every update of the database. Among other parameters, statistics about database growth, average sequence lengths and amino acid composition, taxonomic origin, journal citations and database cross-references are presented, including some graphics.

A new view is available within the SRS Sequence Retrieval System. It displays, for each protein corresponding to a user query, gene name(s) and organism (in addition to the parameters ID, AC, description and sequence length which are displayed by the default view "Short description"). This new view is entitled "Long description" and is available from the menu "Use view ..." in the SRS query form.

The SIB Blast interface (accessible also via "Quick BLAST" or from the bottom of every SWISS-PROT/ TrEMBL entry) now offers the possibility to restrict the similarity search by using taxonomic criteria. A "Taxonomic View" of the results can also be obtained via the BLAST result page.

L'équipe Swiss-Prot a le plaisir de vous présenter le premier article de "Protéines à la Une", sa nouvelle rubrique de vulgarisation scientifique dédiée aux protéines qui font parler d'elles dans l'actualité.

January 18, 2001

SWISS-PROT
New cross-references have been added to three additional databases:

• GlycoSuiteDB - a database of glycan structures; explicit links
  example: P00750
• GeneCensus - a compilation of ORF data for the Saccharomyces genome; implicit links
  example: Q01802
• HUGE - a database of human unidentified gene-encoded large proteins; implicit links
  example: P42330

NiceProt & SIB BLAST The NiceProt view of SWISS-PROT/TrEMBL entries now contains a direct submission button requesting a blastp homology search of the protein against SWISS-PROT/TrEMBL/TrEMBLnew, on the SIB BLAST server ("Quick BlastP search"). In the results of SIB BLAST searches on ExPASy (normal or "NiceBlast" output formats), the user can select a number of matching sequences and directly submit them to a ClustalW search, or retrieve and download the corresponding SWISS-PROT/TrEMBL entries.

Proteomics tools

• FindPept: This new tool can identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage.
• PeptIdent: Several new features have been added.
  • When searching SWISS-PROT, all alternative splice isoforms described in SWISS-PROT feature tables are included in the search (e.g. Isoform 12S of O43184).
  • New organism classes can be searched. For each of the available taxonomic available (e.g. Mammalia), a new section (e.g. other Mammalia) has been added, which comprises all entries not corresponding to any of the searchable subclasses (e.g. all Mammalia except human, bovine, rabbit, and other rodents).
  • For each matching protein in a PeptIdent result, buttons are available which allow further analysis of the protein by direct submission of the data to FindMod, FindPept, GlycoMod, PeptideMass and BioGraph.
• GlycoMod: Possible oligosaccharide structures suggested by GlycoMod are linked to the GlycoSuiteDB database of glycan structures, if they are reported in this database. The user can also select to display compositions reported in GlycoSuiteDB separately from the compositions not known in the database.

October 28, 2000

Several new features have been implemented on ExPASy during the last few months:
• The Swiss Center for Scientific Computing (CSCS) and the Swiss Institute of Bioinformatics provide a powerful and rapid new BLAST server. A submission form to this server is available from the bottom of each SWISS- PROT/TrEMBL entry on ExPASy. Results of blastp similarity searches submitted from this form are now parsed and displayed in a more user-friendly way, including a graphical representation and a link to NiceBlast. NiceBlast is a html table detailing complete descriptions of all matching proteins, including the full protein name, gene name, sequence length and organism.

• Sequences of alternatively spliced isoforms of the same protein are documented in the feature table of that protein sequence record. In collaboration with the SWISS-PROT group at EBI, a program varsplic.pl has been written to generate additional records from SWISS-PROT and TrEMBL, one for each splice isoform of each protein. The resulting data sets for SWISS-PROT and TrEMBL are available on our ftp server, along with a more detailed description of the project and information on how to obtain a local copy of the varsplic.pl program.

  The additional isoform entries have been added to the SWISS- PROT/TrEMBL databases underlying the BLAST server at SIB/CSCS Switzerland, and ScanProsite. Gradually, all other tools on ExPASy will be modified to handle splice isoforms. The NiceProt view of SWISS-PROT/TrEMBL provides links from the isoform name in the feature table (example: Q01432) to a page displaying the sequence of the corresponding isoform.

• In the framework of the HAMAP project, we provide clean non-redundant SWISS-PROT/TrEMBL data sets for all completely sequenced microbial genomes. These files are available on the ExPASy ftp server in SWISS-PROT and Fasta format, and can also be used for similarity searches on the SIB Blast server ("microbial proteomes").

  A Genomic Proximity Viewer is available for those microbial genomes where an ORF numbering system exists. For those organisms, it is possible to click on the ORF name in the SWISS-PROT/TrEMBL GN (gene) lines to obtain a list of proteins encoded by genes in proximity (example: P46448). The tool is also accessible from the HAMAP complete proteome pages of those organisms. Example: Borrelia burgdorferi.

• The following cross-references have been added to relevant SWISS-PROT/TrEMBL entries:
  • InterPro - the Integrated Resource of Protein Families, Domains and Sites, integrating PROSITE, Pfam, PRINTS and ProDom. A link to a graphical view of the domain structure is also available; example: O15197.
  • MEROPS - a peptidase database; example: O96009.
  • NucleaRDB - a database of nuclear receptors (implicit links); example: O09018.
  • DIP - Database of Interacting Proteins (implicit links); example: P10275

• The Compute pI/Mw tool, if called for a list of proteins, can now produce, in addition to the usual verbose format, a table in text format that can be exported to an external application.

• Protein Spotlight is a periodical electronic review from the SWISS-PROT group. It is published on a monthly basis and consists of articles focused on particular proteins of interest. You can subscribe to receive each issue, free of charge, in HTML or PDF format.

April 26, 2000

Proteomics Tools:
• We are happy to announce a new tool in our suite of ExPASy protein identification and characterization tools:
  GlycoMod is a tool that can predict the possible oligosaccharide structures occurring on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides. GlycoMod has been developed in collaboration with Nicolle Packer, initially at Macquarie University, Sydney, and later at Proteome Systems Ltd. GlycanMass is an associated tool which allows to calculate the mass of an oligosaccharide structure from its oligosaccharide composition.
• Detailed documentation is now available for the PeptIdent peptide mass fingerprinting identification tool.
• A number of new functionalities have been added to FindMod:
  • Results can now be obtained by email (as an alternative to receiving them on-line in the browser window), in form of an html file, with exactly the same functionality as for on-line display.
  • Several new enzymes have been added, mainly different versions of Chymotrypsin.
  • Results given in the "potential amino acid substitutions" table have been refined:
    • We no longer suggest amino acid (aa) substitutions occurring on the enzyme cleavage site and substituting the aa for an aa at which the enzyme does not cleave.
    • If the suggested aa substitution corresponds to a sequence variant or conflict as annotated in the SWISS-PROT feature table, this substitution is highlighted in color (green background for that table line), and a hypertext link is provided to the corresponding annotated variant or conflict.
• Compute pI/Mw can now be used with a file uploaded from the user's computer, if this file contains a list of SWISS-PROT/TrEMBL IDs/ACs.

  SWISS-PROT:

• Dotlet, a diagonal dot-matrix program drawing a dotplot of two sequences, has been included in the set of tools that can be called directly from the bottom of each SWISS-PROT/TrEMBL entry on ExPASy. This allows to find repeats within the sequence.
• In the last few months, cross-references to the following databases have been added to relevant SWISS-PROT entries:
  • TubercuList - for entries from Mycobacterium tuberculosis
  • PRINTS - Protein fingerprint database
  • implicit links to BLOCKS - a database of multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins.
  Example entry: Q50705.

• There are 6 new SWISS-PROT documents:
  • humchr08.txt: Index of protein sequence entries encoded on human chromosome 8.
  • humchr09.txt:Index of protein sequence entries encoded on human chromosome 9.
  • humchr10.txt:Index of protein sequence entries encoded on human chromosome 10.
  • humchr11.txt:Index of protein sequence entries encoded on human chromosome 11.
  • dbxref.txt: List of databases cross-referenced in SWISS-PROT.
  • rprowaze.txt: Index of Rickettsia prowazekii strain Madrid E entries.

  ExPASy:
  

• We are happy to announce a new ExPASy mirror site, at Peking University, China: http://expasy.pku.edu.cn/.
  
• We have completely revised the ExPASy server access statistics, which were previously frequently incomplete and erroneous. Every month, a table is updated which lists monthly access statistics for the main Swiss ExPASy server and for all our mirror sites.

October 4, 1999

• The ExPASy server has a new mirror site for North America, at the Canadian Bioinformatics Resource in Halifax, Canada. It can be reached at the URL http://expasy.cbr.nrc.ca/.

• The SWISS-PROT search by description tool has been extended to TrEMBL.
• There are five new SWISS-PROT documents:
  
  • humchr12.txt: an index of protein sequence entries encoded on human chromosome 12.
  • humchr14.txt: an index of protein sequence entries encoded on human chromosome 14.
  • humchr15.txt: an index of protein sequence entries encoded on human chromosome 15.
  • humchr16.txt: an index of protein sequence entries encoded on human chromosome 16.
  • annbioch.txt: SWISS-PROT annotation: how is biochemical information assigned to sequence entries

• When scanning a pattern against the SWISS-PROT/TrEMBL databases using the ScanProsite tool, users can now restrict their searches to an organism or a taxonomic range.
• The NiceSite view of PROSITE (example: PS00101) has been modified to include two new statistical values in its section of numerical results, namely
  Precision (true hits / (true hits + false positives)) and
  Recall (true hits / (true hits + false negatives)).

• A new parameter has been added to the list of parameters computed by the ProtParam tool: The program now calculates the atomic composition of a protein, in addition to molecular weight, theoretical pI, amino acid composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).

June 16, 1999

The 'Nice' view tools for the databases provided on ExPASy (SWISS-PROT, SWISS-2DPAGE, PROSITE, ENZYME) have been developed in order to provide users with an easily readable alternative to the original text file representation.

The following tools are available:

Database       Tool       Example
---------------------------------------------------------------------------
SWISS-PROT     NiceProt   http://www.expasy.ch/cgi-bin/niceprot.pl?P14060

SWISS-2DPAGE   Nice2DPage http://www.expasy.ch/cgi-bin/nice2dpage.pl?P00938

PROSITE        NiceSite   http://www.expasy.ch/cgi-bin/nicesite.pl?PS00661 
                          http://www.expasy.ch/cgi-bin/nicedoc.pl?PDOC00566

ENZYME         NiceZyme   http://www.expasy.ch/cgi-bin/nicezyme.pl?2.4.1.1 

We have now changed all our tools and database search programs on ExPASy to display the 'Nice' version of a database entry by default. The programs displaying database entries in their original text formats continue to be maintained, and links are available from the 'Nice' views to the corresponding get-xxx-entry programs (e.g. get-sprot-entry).

If you maintain pages with links to entries from the above-mentioned databases, you might be interested to update these links to use the 'Nice' View if you prefer this representation to the original format. Otherwise you are, of course, completely free to keep the get-xxx-entry links.

May 24, 1999

• Linking to ExPASy
  We have revised the ExPASy file and directory structure, in order to have the vast amount of data that has accumulated on ExPASy since September 1993 available in a more structured manner, and to facilitate replication on our mirror sites. This has caused certain changes in html links, and we would like to ask our users to update their bookmarks and links accordingly. If in doubt, please refer to the document 'How to create html links to ExPASy'.
  At the same time we wish to reiterate our announcement of the ExPASy mirror sites in Taiwan  and Australia . For your own convenience, please use the mirror site closest to you. Regular users might also bookmark the addresses of all ExPASy mirror sites to use as backup for the rare cases that their favourite ExPASy site is down or unreachable due to network problems.

  Please make sure to update all pointers using the old domain expasy.hcuge.ch, which was replaced by
  http://www.expasy.ch/ in March 1997 (!). The 'expasy.hcuge.ch' address might be disabled in the near future.

• Protein identification tools
  AACompIdent  and MultiIdent  have been revised, and the database choice has been extended to include TrEMBL. Results are now sent to the user in html format (rather than text only), and html links allow direct access to the matching SWISS-PROT/ TrEMBL entries.

• SWISS-PROT cross-references
  SWISS-PROT entries from Escherichia Coli entries with 'DR ECOGENE' lines are now directly linked to EcoGene at the University of Miami.
  There is a new type of cross-reference lines for sequence entries from Brachydanio rerio (Zebrafish): these entries are now linked to the Zebrafish Information Network (ZFIN) at the University of Oregon.

• New features have been added to improve interactivity in accessing SWISS-2DPAGE:
  • All searching functions in the database can be accessed from the top page and results page of each keyword search function (example: search by description). This feature has been designed to facilitate the navigation between the different ways to query the database (by description, by access number, by authors, by full text search).
  • A new tool is provided to retrieve in a table all the protein entries identified on a given reference map, with all 2-DE information: spot serial number, pI, Mw, mapping procedure, references (example).
  • A new way to query the database is provided. From a user-entered amino acids sequence, one can display the estimated location on a choosen reference map (example).

February 26, 1999

• Several new features have been added to the PeptIdent peptide mass fingerprinting identification tool:
  • It is now possible to search SWISS-PROT and/or TrEMBL.
  • In the page displaying the PeptIdent results, a button allows to perform a new search with slightly modified parameters by giving access to the PeptIdent form filled in with all previously used parameters.
  • For each matching protein, a direct link to BioGraph gives access to a graphical representation of the results of the PeptIdent query. BioGraph was developed by Daniel Doubrovkine and Anton Soudovtsev as a student project in the scope of the Bioinformatics course given at Geneva University.
  • The sequence portion covered by the matching peptides can optionally be displayed and highlighted in colour, as well as the difference between pI and Mw values of the matching proteins and the user-specified values.

• In the results of the SIM binary sequence alignment tool, a direct link has been addded to the PRSS program from EMBnet-CH which evaluates the significance of a protein sequence similarity score.

• Direct links have been added from the comments (CC) lines of relevant SWISS-PROT entries to the SWISS-PROT documents listing ribosomal protein families (e.g. RL2_ECOLI), aminoacyl-tRNA synthetases (e.g. SYC_HUMAN) and 7-transmembrane G-linked receptors (e.g. AA3R_MOUSE).

• Since the introduction of organism classification (OC) terms of the NCBI taxonomy with SWISS-PROT release 37, OS (organism species) lines have been linked to the corresponding pages of the NCBI taxonomy browser.

• The PROSITE full text search tool has been improved. Like in the SWISS-PROT/TrEMBL full text search program, wildcards can be used in query strings and search keywords can be combined with boolean operators.

• We have developed Nice2DPage, a tool that provides a user-friendly tabular view of SWISS-2DPAGE entries (example). The 'Nice2DPage View of SWISS-2DPAGE' is accessible from the top of each SWISS-2DPAGE entry on ExPASy.
• New hypertext cross-references have been added to SWISS-2DPAGE entries (e.g. P02997):
  • from the 2D comments lines (MAPPING, EXPRESSION LEVEL...), direct links have been added to the concerned citation in the SWISS-2DPAGE entry
  • from the 2D lines concerning AMINO ACID COMPOSITION and PEPTIDE MASSES data, direct links have been added to the concerned section in the user manual describing data format and protocols.

• Links to the Brenda enzyme database have been added to ENZYME entries.

October 27, 1998

• The SWISS-PROT/TrEMBL and SWISS-2DPAGE full text search tools have been improved. The databases are now indexed using the Glimpse search engine, wildcards can be used in query strings, more fields (line types) are indexed and response times are much shorter than before.

• We have developed NiceProt, a tool that provides a user-friendly tabular view of SWISS-PROT entries (example). The 'NiceProt View of SWISS-PROT' is accessible from the bottom of each SWISS-PROT entry on ExPASy.

• The following database cross-references and literature references have been added to SWISS-PROT entries on ExPASy:
  • DR links to the PRESAGE resource for structural genomics from Stanford University (e.g. P53878);
  • DR links from relevant immunoglobin entries to IMGT, the international ImMunoGeneTics database from the University of Montpellier (e.g. P01876);
  • References to the Worm Breeder's Gazette in the RL lines of relevant entries from Caenorhabditis elegans (e.g. Q09517).

• Users who wish to save and retrieve all SWISS-PROT entries originating from a species can do this via the SWISS-PROT document 'List of organism identification codes': By clicking on any of the species codes (e.g. DROME) and specifying a filename, one can save all corresponding entries to a file which can be retrieved from the anonymous ExPASy FTP server.

• The output format of the PeptIdent peptide mass fingerprinting identification tool has been improved. PeptIdent results now contain a table summarizing information about the matching proteins, from where the user can jump to the detailed listing for the corresponding peptides.

• The new experimental tool CombSearch provides a unified interface for simultaneous queries to several protein identification programs accessible on the web. CombSearch was written by Rémi Hammerli and Pavel Dobrokhotov as a student project in the scope of the Bioinformatics course given at Geneva University.

• A new page providing links to conferences and events is available and accessible from the ExPASy home page. If you know about any conferences on molecular biology or bioinformatics we encourage you to register them.

• The ExPASy interfaces which allow the direct submission of a SWISS-PROT/TrEMBL sequence to BLAST servers at EMBnet-CH and NCBI have been modified to provide a more transparent selection menu of BLAST programs and databases. These programs are designed for similarity searches easily accessible from a SWISS-PROT/TrEMBL entry; for advanced searches with more options we recommend to use the original BLAST submission forms at EMBnet-CH or NCBI.

August 24, 1998

• There is a new tool in our section 'Protein identification and characterization tools':
  PeptIdent allows the identification of proteins using pI, Mw and peptide mass fingerprinting data. Experimentally measured, user-specified peptide masses are compared with the theoretical peptides calculated for all proteins in SWISS-PROT. A species (or group of species) can also be specified for the search. PeptIdent makes extensive use of the annotations in SWISS-PROT and takes into account post-translational modifications as documented in SWISS-PROT.
  Results are displayed on-line or can be sent by email, in form of a html table. The result file contains direct links to FindMod to further characterize matching proteins by predicting potential protein post-translational modifications and finding potential single amino acid substitutions, and to PeptideMass.

• There is a new document describing how to create HTML links to services on ExPASy.

• In July 1998, SWISS-PROT, PROSITE and ENZYME have undergone major releases.

• New hypertext cross-references have been added to SWISS-PROT entries (example: P98073):
  • in RX lines: Medline abstracts corresponding to SWISS-PROT references can now also be consulted at the Weizmann Institute of Science in Israel, in addition to the archives at NCBI, ExPASy and GenomeNet Japan. These links have also been added to SWISS-2DPAGE entries.
  • DR DOMO lines have been added: These links provide direct access to relevant information in the DOMO database of homologous protein domains maintained by Jérôme Gracy at Infobiogen.
  • At the bottom of the page displaying a SWISS-PROT/TrEMBL entry, there are now direct links for submission of the sequence to ScanProsite and ProfileScan.
  • RL lines: Relevant SWISS-PROT entries are now directly linked to the Plant Gene Register, an electronic publication for articles describing the isolation and DNA sequence determination of plant genes (example: P48422).
  • The ExPASy interface to the BLAST server at EMBnet-CH now uses their new BLAST2 client, replacing WU-BLAST.

June 13, 1998

• The ExPASy server presents itself in a new layout: the home page, database entry pages, the tools page and many other pages have been redesigned for easier navigation and better readability.

  Users can now also use (in addition to the home page and ExPASy Index) the newly created clickable ExPASy site map to find useful tools, documents and services available on our server, and to find out about functional links between them.

  A new documentation page has been created which presents a complete table of documents available on ExPASy.

• There are two new SWISS-PROT documents:
  
  • humpvar.txt: an index of human proteins with sequence variants
  • humchr17.txt: an index of protein sequence entries encoded on human chromosome 17.

• Protein domains, chains etc. documented in the SWISS-PROT feature tables, if corresponding to subsequences of at least 10 amino acids, can now be directly submitted to a BLAST similarity search from the pages highlighting these subsequences. Example: DOMAIN EXTRACELLULAR ALPHA-1 (1A24_HUMAN).

• Two bugs have been corrected in ExPASy tools:
  • There was a small error in the computation of extinction coefficients by ProtParam: The contribution of Cysteines to the extinction coefficient (Gill S.C., von Hippel P.H. Anal. Biochem. 182:319-326(1989)) of a protein is only half of the values used previously in ProtParam, which results in slightly different values for the extinction coefficient.
  • Our Translate tool no longer ignores base-ambiguity characters such as M, W, Y, etc. Previously performed translations for DNA sequences containing characters other than A,C,T,U,G, and N are likely to have been incorrect.
  We apologize for any inconvenience caused by these errors and encourage our users to continue to send us their comments and bug reports.

March 27, 1998

• There is a new tool in our section 'Protein identification and characterization tools':
  FindMod is a program for the de novo discovery of protein post-translational modifications. It examines peptide mass fingerprinting results of known proteins for the presence of currently 18 types of PTMs of discrete mass. This is done by looking at mass differences between experimentally determined peptide masses and theoretical peptide masses calculated from a specified protein sequence. If a mass difference corresponds to a known PTM not already annotated in SWISS-PROT, "intelligent" rules are applied that examine the sequence of the peptide of interest and make predictions as to what amino acid in the peptide is likely to carry the modification.

• Improved tools:
  PeptideMass, which calculates masses of peptides and their posttranslational modifications for a given protein sequence, can now consider up to 3 missed cleavages. Post-translational modifications may be specified for a sequence in raw sequence format, and substitution tables are available to simplify the interpretation of the results for peptides concerned by database conflicts, variants or splicing variants.

  TagIdent can now search in SWISS-PROT, TrEMBL or both databases. It is also possible to perform an additional scan of a short sequence tag against all fragments contained in the database(s), even if pI and Mw cannot be computed for these proteins.

  MultiIdent (identification using pI, MW, amino acid composition, sequence tag and peptide mass fingerprinting data) is available for constellation 2 (Ala, Ile, Pro, Val, Arg, Leu, Ser, Asx, Lys, Thr, Glx, Gly, Met, His, Phe and Tyr. (Asp+Asn=Asx; Gln+Glu=Glx; Cys and Trp are not considered)) and constellation 4 (like constellation 2, but Gly is not considered).

• Several months ago, we started to distribute and update weekly, a set of data files that can be used to build a non-redundant protein sequence database consisting of SWISS-PROT, TrEMBL and TrEMBL updates. There is now a document explaining the contents and principles of this database.

• Information about the current release and update status of SWISS-PROT has been added to the SWISS-PROT page (currently 'Release 35 and updates up to 20-Mar-1998: 71198 entries').

• New hypertext cross-references have been added to SWISS-PROT entries:
  • in RX lines: Medline abstracts corresponding to SWISS-PROT references can now also be consulted on the Japanese GenomeNet server in addition to the archives at NCBI and ExPASy.
  • in DR PDB lines: Local copies of PDB entries are available. The user is now given the choice between accessing 3D structure information (e.g. 2hhe) in Geneva or Brookhaven (US). Both links provide direct access to 3D structure information in various formats, as well as hypertext links to servers offering related information.
  • DR PROTOMAP lines have been added: These links provide, for a SWISS-PROT entry, a cluster (group) of related proteins as classified by the ProtoMap server at Hebrew University, Jerusalem.
  Example: DEFN_HUMAN.

• SWISS-2DPAGE is now available to be searched by the SRS Sequence Retrieval System.

February 13, 1998

• The SWISS-PROT full text search tool has been redesigned and improved. Boolean operators (AND, OR, NOT) can be used to combine and restrict queries, and special characters such as _ - # ' ( ) , . / are allowed as part of words (as used in SWISS-PROT).

• SWISS-PROT author names (RA lines) have been linked to a page listing all SWISS-PROT entries which contain references to articles (co-) authored by this author.

• The ExPASy interface to the EMBNet-CH BLAST server now contains a new option: This BLAST process manages two job queues: a (presumably) fast one and a slow one. Based on the sequence provided and the database requested, the process makes an (educated ???) guess to decide if the query will require more than 5 minutes of CPU time. Small jobs are allowed to proceed in the fast queue, while the others are forced to the slower one. If an e-mail address is provided, results of slow jobs will be automatically mailed back, while fast jobs will proceed as before.

• Two features have been added in SWISS-2DPAGE to facilitate visualisation and differentiation of spots:
  
  • If you click on a spot in one of the SWISS-2DPAGE maps (e.g. Plasma), the '2D' line describing this spot in the corresponding SWISS-2DPAGE entry is highlighted in green.
    
  • Hypertext links have been added from spot serial numbers on SWISS-2DPAGE '2D' lines to the master image for the protein, in which the spot with this serial number is highlighted in green (in contrast to the other spots displayed in red). Example: P00450.

January 13, 1998

• Since November 1997, SWISS-PROT, PROSITE, ENZYME and SWISS-2DPAGE have all gone through major releases.

• There is a new program that allows you to randomly retrieve a SWISS-PROT or TrEMBL entry.

• A new output format option has been added to our Translate tool. When translating a nucleotide sequence into a protein sequence, you can now also select to include, for each of the six open reading frames, the nucleotide sequence in the output.

• Cross-references and direct links to the Mendel Plant Gene Nomenclature Database have been added in corresponding SWISS-PROT entries. Example: P12084. There also is a file containing all SWISS-PROT entries with cross-references to Mendel in our series of "special selections", which is updated weekly and can be downloaded from our anonymous FTP server.

• Proteins which are documented to belong to an uncharacterized protein family in the SWISS-PROT CC (comments) lines, have been linked to the SWISS-PROT document upflist.txt. Example: P55061.

November 27, 1997

• In SRS (Sequence Retrieval System), SWISS-PROT DR (Database crossReference) and RC (Reference Comment) lines have been indexed. You may search for e.g. all entries with cross references to PDB (enter 'PDB' in the DbName field), or all proteins that have been found in E.coli strain K12 (enter 'K12' in the 'RefComment' field).

• It is now possible to retrieve a number of SWISS-PROT/TrEMBL entries by specifying a list of accession numbers or entry names (ID).

• There are 4 new SWISS-PROT documents:

  humchr18.txt: an index of protein sequence entries encoded on human chromosome 18;

  pcc6803.txt: an index of Synechocystis strain PCC 6803 entries;

  deleteac.txt: an index of deleted accession numbers.

  upflist.txt: UPF (Uncharacterized Protein Families) list and index of members.

October 7, 1997

• We have implemented a search index, ExPASy Index, to help you find information within the ExPASy server. The index contains all the documents of ExPASy (currently about 800), except the database entries. It has been automatically indexed by the Marvin robot.
  Our new service BioHunt uses the same concept and allows you to search the internet for molecular biology information. In the current version, 17136 documents have been indexed.

• The ScanProsite tool has been modified to work with TrEMBL as well as SWISS-PROT. Furthermore, the part of the program which allows to scan a pattern against SWISS-PROT (and TrEMBL) has been improved and now avoids the previously frequent 'Document contains no data' error for large scan results.

• In PeptideMass, the set of post-translational modifications with discrete mass differences considered in peptide mass computation now also contains O-GlcNac (documented as FT CARBOHYD GLCNAC in SWISS-PROT) and C-Mannosylation of Tryptophan (FT CARBOHYD C-MANNOSYL). Thus, 17 post-translational modifications are now considered in PeptideMass. For examples, try CRAA_BOVIN or RNKD_HUMAN, don't forget to select "display all known post-translational modifications" and click on the "Perform" button.

• There is a new SWISS-PROT document:
  mgdtosp.txt - Index of MGD entries referenced in SWISS-PROT.

• Hyperlinks have been added from SWISS-PROT entries to the TIGR Microbial Database, which provides links to the information provided by TIGR on the genes encoded in the genomes they have sequenced (so far these are: Haemophilus influenzae, Helicobacter pylori, Methanococcus jannaschii, and Mycoplasma genitalium). (Example: FDHB_METJA)
  We have also created a specific file containing all SWISS-PROT entries containing cross-references to the TIGR database in our series of "special selections", which is updated weekly.

• SWISS-PROT reference (RL) lines and PROSITE references referring to one of the journals available at IDEAL, an online electronic library containing all 175 Academic Press journals, now contain direct links to the IDEAL server if the article was published in 1996 or later. From this, a 'Guest login' leads to the abstract of the article. (Example: RGSE_RAT)
  

September 5, 1997

Some new features of ExPASy:

• The PeptideMass program has been modified to take into account up to 2 missed cleavage sites. A new column 'MC' has been added to the output which indicates the number of missed cleavages, and peptides resulting from 0, 1 or 2 missed cleavages are displayed in different colours.
• A new parameter has been added in the ProtParam program: ProtParam results now include the grand average of hydropathicity (GRAVY) for a given protein.
• At the bottom of each SWISS-PROT and TrEMBL entry, there is now a link to a page displaying the entry in FASTA format (example: P11553).
• The local submission form to the WU-BLAST server at Lausanne has been changed to use as the default database the set of non-redundant protein databases SWISS-PROT, TrEMBL and TrEMBL_NEW.
• There are two new SWISS-PROT documents:
  - metallo.txt - Classification of metallothioneins and index of MT entries
  - hpylori.txt - Index of Helicobacter pylori strain 26695 chromosomal entries
• The display of current and previous Swiss-Flash bulletins has been redesigned: A table is available which lists all Swiss-Flash bulletins by category, including date, title and author of the bulletins.

July 24, 1997

We have now an SRS server (version 5) running on ExPASy. SRS (Sequence Retrieval System) allows you to retrieve entries across multiple databases with more sophisticated criteria than those allowed by the text-search interfaces available from the SWISS-PROT top page.

You can combine all the fields with logical operators and achieve queries like:

• Give me all vertebrate proteins having a PH domain and that are longer than 1000AA or
  
• Give me all calcium-binding proteins localized in the endoplasmic reticulum.

Five databases are indexed: SWISS-PROT, TrEMBL, TrEMBL_NEW, PROSITE, and ENZYME. SWISS-PROT and TrEMBL are updated on a weekly basis so that the set of these two databases stays non-redundant.

TrEMBL entries are now fully accessible on ExPASy via a cgi-script. The hypertext version of TrEMBL contains links to various databases and allows direct access to sequence analysis tools such as Swiss-Model, Blast, ProtParam, ProtScale, Compute pI/Mw and PeptideMass, as is the case for SWISS-PROT.

If you wish to link to a TrEMBL entry, you can use the following URL:

http://www.expasy.ch/cgi-bin/get-sprot-entry?<TrEMBL-AC>

e.g. to create a link to TrEMBL entry Q00061, use:

http://www.expasy.ch/cgi-bin/get-sprot-entry?Q00061

June 6, 1997

We are actively seeking any type of updates and/or corrections of SWISS-PROT entries, whether they have been published or not, and we encourage our users to submit us their suggested updates or corrections. This can be done using our new submission form, which can be accessed through an active link from the SWISS-PROT home page or from the bottom of each SWISS-PROT entry. Please read the tips and guidelines to find out what type of information we are seeking and how to proceed. We would already like to thank our users in advance for any contribution they can make in updating and correcting SWISS-PROT!

The tool which allows you to visualize and highlight the subsequence corresponding to a line in a SWISS-PROT feature table (FT) has been improved and is now using colour to highlight the subsequences in question. Example: in FA9_HUMAN:

FT   DOMAIN       93    129       EGF-LIKE 1, CALCIUM-BINDING (POTENTIAL).

May 21, 1997

At the bottom of each page displaying a SWISS-PROT entry, you will now find a link to a graphical Feature Table viewer (Java Applet) written by Thomas Junier at the Bioinformatics Group of ISREC Lausanne.

We have added several new hyperlinks in SWISS-PROT entries:

The DR lines containing cross-references to EMBL/GenBank/DDBJ now include a link to a page displaying exclusively the corresponding CoDing Sequence (CDS).

The RL lines referring to recent articles in certain journals whose WWW servers are maintained in collaboration with HighWire Press are now active hyperlinks to the abstracts of the corresponding articles. From the abstract page you can frequently access directly a full text on-line version of the article. The journals include J. Biol. Chem., Proc. Natl. Acad. Sci. USA, Science, Cell, etc.

Entries with cross-references to MIM are now also linked (through a new virtual "DR GeneCards" line) to GeneCards, a database integrating information about the functions of human genes and their products, and of biomedical applications based on this knowledge.
Example: BRC1_HUMAN.

Entries belonging to family 1 of G-protein coupled receptors (as documented in feature tables) now contain active links to GPCRDB-Snakes diagrams (through the new virtual "DR GPCRDB-Snakes" line) prepared by the GPCRDB group at EMBL Heidelberg.
Example: 5H1A_HUMAN.

There are 3 new SWISS-PROT documents:

humchr19.txt: an index of protein sequence entries encoded on human chromosome 19

ngr234.txt: a table of putative genes in Rhizobium plasmid pNGR234a

initfact.txt: a list of translation initiation factors

On the ExPASy anonymous FTP server, the SWISS-PROT update files new_seq.dat, upd_ann.dat and upd_seq.dat are now also available in compressed form in the directory /ftp/databases/swiss-prot/updates_compressed/.

March 27, 1997

We have modified and improved access from ExPASy to various BLAST (Basic Local Alignment Search Tool) similarity search services:

In the tools page, you can now choose between 5 different interfaces to BLAST servers in Switzerland, the USA and Germany:

Switzerland:

Running on a 2-processor Pentium Pro machine, the new WU-BLAST server at EMBNet Switzerland in Lausanne has a faster response time than the EPFL server, and should be more stable. As opposed to the original NCBI BLAST algorithm, WU-BLAST generates gapped alignments. A full set of weekly updated databases is provided.

• Local interface to WU-BLAST at EMBNet-CH (Lausanne)
• Original interface to WU-BLAST at EMBNet-CH (Lausanne)

USA:

• Local interface to BLAST at NCBI
• Original interface of BLAST at NCBI

Germany:

• WU-BLAST at Bork's group in EMBL (Heidelberg)

For direct BLAST submission from a SWISS-PROT entry (icons at the bottom of the page displaying an entry - example), you have the choice between the servers at NCBI and EMBNet-CH.

The following documents have been added to the list of SWISS-PROT documents:

• bloodgrp.txt - Blood group antigen proteins
• fly.txt - Index of Drosophila entries and their corresponding FlyBase cross-references
• mjannasc.txt - Index of Methanococcus jannaschii entries
• mgenital.txt - Index of Mycoplasma genitalium strain G-37 chromosomal entries

March 17, 1997

We have completely rewritten the Swiss-Shop sequence alerting system for SWISS-PROT that allows you to automatically obtain (by email) new sequence entries relevant to your field(s) of interest.

In the new version of Swiss-Shop, some new features have been added:

As before, you can either launch a sequence/pattern based search or a keyword based search.

• For a sequence based search, you need to specify a SWISS-PROT ID or AC or a raw protein sequence, and your sequence will be scanned, at each weekly update of SWISS-PROT, against the new sequences in the database using the alignment program BLAST. Sequences thus found to be similar to your protein will be sent to you by email. It is up to you to specify the BLAST probability threshold for P(N) (the probability that the alignment is real and not random), and you will receive a list of all sequences for which this probability is below the specified value.
• For a pattern based search, enter a PROSITE ID or AC or a pattern in PROSITE format, and Swiss-Shop will scan this pattern, at each weekly update of SWISS-PROT, against the sequences that have been added in SWISS-PROT since the last weekly update. You will receive the list of new entries matching your pattern.
• For a keyword based search, it was previously possible to specify keywords from SWISS-PROT OS, OC, OG (taxonomy), RA (authors), KW, DE, CC lines. In addition to these lines, you can now also search DR (Cross-references to other databases) and FT (feature) lines with one or more specified keywords. Swiss-Shop will look for these keywords on the corresponding lines of all SWISS-PROT entries added in the database since the last weekly release.

Furthermore, we now offer you 4 different output formats. You can choose to receive the sequences matching your query

• as a file in SWISS-PROT format or
• as a list of SWISS-PROT accession numbers or
• in form of a short report containing information from SWISS-PROT ID, AC, DE, OS lines or
• as a list of SWISS-PROT accession numbers with hypertext links to the corresponding entries on the ExPASy WWW server. This allows you to view your email message with your Web browser and to follow the hypertext links to the full entries on ExPASy.

You can further specify if you wish to be notified every time Swiss-Shop is run, even if there are no new sequences matching your query, or to receive an email report only when there are new SWISS-PROT entries matching your search terms.
You can specify the expiration date of your request, the default being one year after submission.
For editing previous requests (e.g. to update the expiration date or to modify search criteria) you can enter a password for each new request. This allows you to open the request later and edit it on-line rather than deleting it and submitting a new one.

March 6, 1997

New and improved protein identification tools:

There is a new tool on ExPASy:
• MultiIdent: This tool achieves protein identification using parameters such as protein species, estimated pI and MW, AA composition, sequence tag, and peptide mass fingerprinting data. It is particularly suited to the identification of proteins across species boundaries. Currently, the program works by first generating a set of proteins in the database with AA compositions close to the unknown protein, as for AACompIdent. Theoretical peptide masses from the proteins in this set are then matched with the peptide masses of the unknown protein to find the number of peptides in common (number of "hits"). Three types of lists are produced in the results. Firstly, a list where proteins from the database are ranked according to their AA composition score; secondly, a list where proteins are ranked according to the number of peptide hits they showed with the unknown protein; and thirdly, a list that shows only proteins that were present in both the above lists, where these proteins are ranked according to an integrated AA and peptide hit score. In all these lists, protein pI, MW, and species of origin (using a term from SWISS-PROT OS or OC lines) and keywords can be used, as in AACompIdent, to increase the specificity of searches.

  The following tools have been improved, offering numerous additional features:

• AACompIdent (identification of a protein from its amino acid composition)
  You can restrict your search by specifying one or more term(s) from the OS or OC lines of SWISS-PROT (example: HOMO SAPIENS or MAMMALIA). You can also enter a keyword appearing on the KW lines of SWISS-PROT to further restrict your search. For example, a keyword of "CALCIUM-BINDING" could be used in conjunction with the OC term "MAMMALIA" to see if a user- entered protein matches well with any mammalian calcium-binding proteins in the database.
• TagIdent now allows, for one or more species (term from SWISS-PROT OS or OC lines) and with an optional keyword,
  1. the generation of a list of proteins close to a given pI and Mw,
  2. the identification of proteins by matching a short sequence tag of up to 6 amino acids against proteins in the SWISS-PROT database close to a given pI and Mw,
  3. the identification of proteins by their mass, if this mass has been determined by mass spectrometric techniques.
  

  For PeptideMass, Compute pI/Mw, AACompSim and all the above-mentioned tools, documentation and references have been added and the submission forms have been reformatted and improved.

March 4, 1997

Thanks to the generosity of the Geneva Government, we have been able to acquire a new computer for the ExPASy server (a Sun Microsystems Ultra Server Enterprise 2). The server is now accessible at URL:

http://www.expasy.ch

The old URL remains valid for some time.

January 9, 1997

Some new features of ExPASy:

• New active links have been established from SWISS-PROT entries
  • to the TRANSFAC database of transcription factors;
  • from Bacillus subtilis entries to Micado (MICrobial Advanced Database Organization) at INRA, France;
  • to local copies of MEDLINE abstracts. We now give the user the choice of retrieving a MEDLINE abstract (example: 90368558) from either NCBI or Geneva;
  • to our Peptide Mass tool which cuts a protein sequence with a chosen enzyme and computes the masses of the received peptides.
• From Release 35 on, SWISS-PROT comments (CC) lines can contain a new 'topic' "DATABASE", which contains information about related databases catering for a specific protein or a for a very limited number of proteins. Most of these databases are mutation databases, reporting defects linked to a genetic disease. If such a database is available electronically, the CC DATABASE lines provide the relevant electronic coordinates, e.g. in P29965 (CD4L_HUMAN):

  CC   -!- DATABASE: NAME=CD40Lbase; NOTE=European CD40L defect database;
  CC       WWW="HTTP://www.expasy.ch/cd40lbase/";
  CC       FTP="ftp.expasy.ch/databases/cd40lbase".

• There is a new SWISS-PROT document:
  yeast13.txt - a list of Yeast Chromosome XIII entries.
• Two new features have been added in ENZYME entries:
  • direct links from an enzyme to all relevant maps of Boehringer Mannheim's Biochemical Pathways and
  • links to the WIT (What Is There) database of metabolic pathways.

November 26, 1996

The Boehringer Mannheim Biochemical Pathways maps and index have been digitised and are now accesible on this server. Enter a keyword (such as, for example Oxoacyl) and surf on the biochemical pathways maps.

November 11, 1996

CD40Lbase, The European CD40L Defect Database prepared by Manuel Peitsch, has been made accessible through this server. The purpose of CD40Lbase is to collect clinical and molecular data on CD40 ligand defects leading to X-linked Hyper-IgM syndrome.

A new tool is available from the Tools page: The PeptideMass Peptide Characterisation Software. This program is designed to calculate the theoretical masses of peptides generated by the chemical or enzymatic cleavage of proteins, to assist in the interpretation of peptide mass fingerprinting and peptide mapping experiments. Protein sequences can be provided by the user or can be a code name for a protein in the SWISS-PROT protein database. When proteins of interest are specified from SWISS-PROT, the program considers all annotations for that protein in the database, and uses these in order to generate the correct peptide masses and warn users about peptides that are not likely to be found when undertaking peptide mass fingerprinting. Many protein post-translational modifications which affect the masses of peptides can thus be taken into consideration.

In PROSITE and Enzyme, we have added the possibility to save all referenced SWISS-PROT entries to a file on our anonymous FTP server (in the outgoing directory).

The Compute pI/Mw tool has been included in the list of sequence analysis tools that can be directly accessed from a SWISS-PROT entry.

Two new SWISS-PROT documents are available:
- humchr20.txt - an index of protein sequence entries encoded on human chromosome 20
- tisslist.txt - a list of the currently valid values for the "TISSUE" topic of the RC line type in SWISS-PROT.

September 30, 1996

A new SWISS-PROT document has been added: ribosomp.txt - an index of ribosomal proteins classified by families on the basis of sequence similarities.

In ec2dtosp.txt, an index of E. coli Gene-protein database (ECO2DBASE) entries referenced in SWISS-PROT, we have established direct links to ECO2DBASE, and SWISS-PROT entries now also contain links to ECO2DBASE.

At the end of each page displaying a SWISS-PROT entry we have added links to our sequence analysis tools ProtParam and ProtScale,which allows the user to directly submit the SWISS-PROT sequence to these tools.

September 19, 1996

Some new features of ExPASy:

• We have created a new protein identification tool called TagIdent. This is a modification of the old tool GuessProt. The user can now identify proteins from 2-D gels by giving protein pI and MW estimates, a species or organism classification of interest, and a short sequence tag of up to 6 amino acids. This tag can be derived from the N-terminus, the C-terminus or from internal peptides of a protein. The results are now sent to the user by e-mail, allowing many searches to be done at the same time. If you only want to generate a list of potential proteins in a specific pI or MW range (as was the function of the old tool GuessProt), do not select the TAG option in the form.
• An email option has been added to the tool ScanProsite: if you want to scan a pattern against SWISS-PROT, you have now the option of having sent the results of your query by email, which should avoid previously frequent timeout problems and is particularly useful for complex patterns.
  ScanProsite, which only scans SWISS-PROT with PROSITE pattern entries (as opposed to rule and matrix entries), can now also be used with the PROSITE rule entry PS00013, PROKAR_LIPOPROTEIN.
  
• SWISS-PROT entries have been linked to DDBJ, the DNA Data Bank of Japan. We have also added direct links to the Bacillus subtilis genomic data bank, SubtiList and to the Yeast Protein Database YPD to relevant SWISS-PROT entries.
• Links have been established from most feature (FT) lines of SWISS-PROT entries to pages that highlight the subsequence in question, both in 1- and in 3-letter amino acid codes.
  Example: in FA9_HUMAN:

  FT   DOMAIN       93    129       EGF-LIKE 1, CALCIUM-BINDING (POTENTIAL).

• We have added three new SWISS-PROT documents:
  humchrx.txt - an index of protein sequence entries encoded on human chromosome X
  yeast7.txt - a list of Yeast Chromosome VII entries
  yeast14.txt - a list of Yeast Chromosome XIV entries.
  
• 2D Hunt, a database created and continuously updated by the Marvin robot contains sites related to electrophoresis and specifically to 2-D electrophoresis. It is now searchable from the SWISS-2DPAGE top page.

April 11, 1996

AACompIdent: New options - AACompIdent is a tool which allows the identification of a protein from its amino acid composition. It searches SWISS-PROT for proteins, whose amino acid compositions are closest to the amino acid composition given. Two new options and a new constellation have been added to this tool:

A. C-Terminal display in tagging option

The user may now choose between displaying the C or N terminal side of the proteins that score best.

B. Permutation search in tagging option

This option searches for all permutations of the given tag in the sequences.

C. Constellation 4

Constellation 4 has been added: Ala, Ile, Pro, Val, Arg, Leu, Ser, Asx, Lys, Thr, Glx, Met, His, Phe and Tyr. (Asp+Asn=Asx; Gln+Glu=Glx; Gly, Cys and Trp are not considered).

March 22, 1996

We have added a new tool, ProtScale which allows you to compute and represent the profile produced by an amino acid scale on a selected protein. 50 scales are provided, including 'classics' such as the Kyte and Doolittle hydrophobicity scale.

Links have been added between relevant SWISS-PROT entries and the 2D gel protein databases at Harefield.

A new SWISS-PROT document has been added which describes the nomenclature of glycosyl hydrolases (GH) and that includes an index of sequences that belong to the various GH families.

A PC (MS-Windows) version of LALNVIEW (graphical viewer for pairwise alignments) is now available.

Nicolas Guex has produced a new logo for PROSITE.

February 16, 1996

We have added a new tool, SIM which computes a user defined number of best non-intersecting alignments between two sequences. The results of the alignment can be viewed graphically using the LALNVIEW program developed by Laurent Duret and which is currently available for Macs and UNIX.

Additional links have been added in the tools page, notably to the Weizmann Institute ultra-fast rigorous (Smith/Waterman) similarity searches using the Bioccelerator and to the Garnier, Osgoodthorpe and Robson (GOR) secondary structure prediction method at SBDS.

The SeqAnalRef database now includes a section listing author's email and eventually also WWW home pages. It is also possible to access the links from a page displaying either a reference list or a single reference.

Amos has recently started to create a list of Biomolecular servers for his own usage, but as some people have asked to access this list (which is under construction), we are making it available from the ExPASy top page. Many other small changes were carried out in the last two months.

We thank you for using ExPASy (we have now reached a cumulative total of 4 million connections).

December 14, 1995

After 29 months of existence the ExPASy molecular biology server received a new logo, designed and produced by Nicolas Guex.

October 23, 1995

The Melanie page has been reorganised. With the announcement of release 2.1 of the Melanie II 2-D PAGE analysis software package, a complete up-to-date description of the software as well as a comprehensive tutorial are now available.

October 13, 1995

Links have been added between SWISS-PROT Escherichia coli K12 chromosomal entries and the EcoCyc database, the encyclopedia of E. coli Gene and Metabolism.

You can now seach in PROSITE by citation.

October 9, 1995

Some new features of ExPASy:

• Search in SWISS-PROT by citation - When you call this option, you are prompted to enter the name of a journal and optionally a volume number and/or a year. The program is written in such a way that you can enter either the full name of a journal or its official abbreviation.
• RandSeq - a new tool to generate random protein sequences.
• SWISS-PROT document haeinflu.txt - Index of Haemophilus influenzae RD chromosomal entries and gene names with links to the TIGR and EMBL servers.
• SWISS-PROT document submit.txt - Description of how to submit sequence data to the SWISS-PROT data bank.
• SWISS-PROT document aatrnasy.txt - List of aminoacyl tRNA synthetases.
• Swiss-Jokes - A new page to give access to our collection of jokes from the fields of molecular biology and of computing.

Many other changes have been done, such as the redesign of the Geneva local pages; the addition, in the tool page, of a link to ProfileScan.

It should also be noted that when you search in SWISS-PROT by either description or by full text and that your seach criteria returns more than two entries, you can save these entries to a file on our anonymous FTP server (in the outgoing directory).

September 19, 1995

AACompIdent: New options - AACompIdent is a tool which allows the identification of a protein from its amino acid composition. It searches SWISS-PROT for proteins, whose amino acid compositions are closest to the amino acid composition given. A new option and a new constellation have been added to this tool:

A. Tagging option

With this option, the first 40 amino acid of each protein are printed in the result, instead of the protein name. One may optionnally also enter a tag (a short seuqnece, typically 3 to 8 residues) which will be matched with the sequences of the resulting proteins. Proteins matching the tag will be marked.

B. Free constellation

This is a free constellation, that is one may select any amino acid constellation he/she likes. One just have to fill in the composition values for the selected amino acids. The values will then be normalised, so that the total make 100 (percent).

September 4, 1995

A new page has been created: WORLD-2DPAGE is an index to all known federated 2-D PAGE database servers, as well as to 2-D PAGE related servers and services.

July 22, 1995

A new tool has been implemented on ExPASy, ProtParam allows the computation of various physical and chemical parameters for a given protein stored in SWISS-PROT or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, extinction coefficient, estimated half-life, instability index and aliphatic index

The Journal of Biological Chemistry (JBC) has a WWW server where abstracts and full text of articles are made available. We are happy to announce the implementation of what we believe to be the first direct link in a sequence database between a reference and the full text version of a cited article. Recent JBC references are directly linked to the corresponding entry point in the JBC server. If you want to see such a link, take a look at reference 3 in SWISS-PROT entry KDSA_ECOLI.

The SWISS-PROT document file jourlist.txt which provides information on all the journals cited in that database, now contains links to WWW or Gopher servers set up by a variety of publishers of academic journals.

Two new SWISS-PROT document have been added, one is a nomenclature and index of peptidase sequences, the other is the list of Yeast Chromosome VI entries in SWISS-PROT

June 19, 1995

A new tool has been implemented on ExPASy, ScanProsite allows to either scan a protein sequence the occurence of patterns stored in the PROSITE database or to scan the SWISS-PROT database - including weekly releases - for the occurence of a pattern.

We are happy to announce a new ""service"" Swiss-Quiz The principle of this quiz is to answer to 10 randomly chosen questions relative to the fields of molecular biology, biochemistry and genetics. Each month, we will randomly pick up one person among all those that have obtained a perfect score (and it's not so easy !) and will send that person some delicious Swiss chocolate !

Links have been added from SWISS-PROT to the Saccharomyces genomic database (SacchDb) at Stanford.

A new SWISS-PROT document has been added, it is a nomenclature and index of allergen sequences.

May 26, 1995

A new service is available: SWISS-2DSERVICE. The Two-Dimensional Gel Electrophoresis Laboratory of Geneva, Switzerland, is running a highly reproducible method for the two-dimensional separation of proteins. The laboratory now provides a 2-D PAGE service to which you may send your samples for analysis. This service includes analytical and preparative high-resolution 2-D PAGE, electrotransfer on membranes and/or amino acid composition.

May 17, 1995

New link in the Tools page to the multiple sequence alignment at Washington University.

May 11, 1995

Two links have been added to the SWISS-PROT entries. The first one directly submits a request to Swiss-Model for a 3D model of the current SWISS-PROT protein. The result is then sent back by e-mail. The second one allows to perform a sequence alignment with the current sequence, using NCBI's Basic Local Alignment Search Tool. This link is especially interesting in the virtual SWISS-PROT entries produced by the Translate tool.

May 5, 1995

We announce a new service, SWISS-FLASH, that reports news of databases, software and services developments from the Swiss biocomputing groups responsible for the ECD, ENZYME, LISTA, PROSITE, SeqAnalRef, SWISS-2DPAGE, SWISS-3DIMAGE and SWISS-PROT databases; the Melanie software package; the WWW ExPASy server; the SWISS-Model, SWISS- Shop and other network-based computational tools; and the SWISS-2DSERVICE services. If you subscribe to this service, you will automatically get the SWISS-Flash bulletins by electronic mail.

The SWISS-3DIMAGE database has been completely reorganised and indexed. The database is now searchable in the same way as the other SWISS-*** databases. We now also supply pictures in JPEG format, in addition to GIF and SGI. The images may still be downloaded by FTP.

Links to REBASE points now the version maintained at John Hopkins, whose layout is nicer than our own text based version !

April 19, 1995

We added Translate, a new tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.

Most of the pages in the server have been "refreshed" to make them more readable.

March 21, 1995

Links have been added from SWISS-PROT to the LISTA database of budding yeast (Saccharomyces cerevisiae) genes coding for proteins prepared under the supervisation of Patrick Linder.

March 7, 1995

Links have been added from SWISS-PROT to the HSSP database of structure-sequence alignments from the Protein Design Group, EMBL, Heidelberg.

March 2, 1995

During the last two months, various links have been added:

• from SWISS-PROT to the SubtiList and YEPD databases
• from ENZYME to PROSITE and to the Ligand database in Kyoto
• internally from PROSITE entries to other relevant PROSITE entries

Links from SWISS-PROT to FlyBase use the new WWW server for that database.

Many new SWISS-PROT documents have been added.

The page on the Melanie 2-D PAGE analysis software has been completely redesigned and includes now a on-line tutorial, as well as a request for information form.

December 7, 1994

In order to help users navigate through the ExPASy server, we have added graphical examples. More will be added in the future. See for example: Celegans examples or the who's who on ExPASy page. Thanks to Brigitte Boeckmann for the illustrations.

October 31, 1994

ENZYME: the ENZYME Data Bank has been added to the ExPASy server. This database may be accessed by EC number, name, compound, cofactor, comment, or by browsing through the list of classes, subclasses and sub-subclasses. Any entry in SWISS-PROT that contains an EC number in the DE line has also a direct link to ENZYME (by clicking on the EC number).

October 20, 1994

New services:

• Swiss-Shop - a sequence allerting system for Swiss-Prot that allows you to automatically obtain new sequence entries relevant to your field(s) of interest.
• Swiss-Model - an automated knowledge-based protein modelling server.

Compute pI/Mw: the tool to compute pI and Mw now accepts also a list of ID/AC's.

SWISS-PROT: in PDB cross-reference lines, there is now a link called RASMOL, sending the PDB entry as a chemical / pdb MIME type. On Unix systems, if you add, in the file .mailcap in your home directory, a line of the form

chemical/pdb; rasmol %s

then RASMOL will automatically be launched to display the protein 3D structure. This works also with any other program which accepts PDB coordinates. On systems other than Unix, this may also be specified. See your browser's manual.

October 13, 1994

The SWISS-PROT top page has been re-modeled. A number of new functionalities and documents have been added.

October 7, 1994

New tools have been added:

• Amino acid composition similarity search - the search may now also be performed from a given SWISS-PROT entry, whose amino acid composition will be compared with the whole SWISS-PROT database.
• Compute pI/Mw - Compute the theoretical pI and Mw from a SWISS-PROT ID or AC, or for a given sequence.

October 5, 1994

The gels run during the 2-D PAGE courses in Geneva are now displayed on the server.

September 29, 1994

SWISS-2DPAGE: protein maps now have a pI/Mw scale.

SeqAnalRef: the Sequence Analysis Bibliographic Reference database has been added to the ExPASy server. This database may be accessed by keyword, by reference identifier, by author and by full text search.

List of on-line experts: in SWISS-PROT and PROSITE top pages, a list of on-line experts gives you the possibility to directly send questions to any of the listed experts. The list is ogranized by subjects.

SWISS-PROT: new lists added:

• List of abbreviations for journals cited
• List of species has been made active
• Yeast Chromosome III entries in SWISS-PROT
• Nomenclature of extracellular domain
• List of on-line experts

PROSITE: new 3D line with active links to PDB.

September 26, 1994

In the tool AACompIdent for identifying a protein by its amino acid composition, options have been added. They allow to specify how many proteins should be displayed, as well as the pI and Mw range in which the search should be performed.

Also, some old bugs have now been corrected.

September 12, 1994

The tool AACompIdent for identifying a protein by its amino acid composition, has been corrected and is now supposed to work. If you still encounter problems, please send us a mail.

June 17, 1994

SWISS-PROT: added cross-references (DR lines) to GenBank.

June 16, 1994

SWISS-PROT: added cross-references (DR lines) to MaizeDB Maize Genome Database of the National Agricultural Library.

June 6, 1994

Added the PROSITE page: PROSITE entries may now be searched by description of sites and pattern, by accession number, by author, and soon by full text search.

June 3, 1994

Added the GuessProt tool to the tools page: you may now get the SWISS-PROT proteins closest to a given pI and Mw.

May 27, 1994

In SWISS-PROT entries, added links to GCRDb - the G-Protein--Coupled Receptor DataBase.

Added the list of nomenclature related references for proteins to the SWISS-PROT top page.

May 26, 1994

Added a new reference 2-D PAGE map of Platelet to SWISS-2DPAGE.

May 20, 1994

The SWISS-2DPAGE team is now organizing a 2-D PAGE training in Geneva once every three months.

May 18, 1994

Added the Yeast Chromosome XI list of proteins to the SWISS-PROT documentation page.

May 11, 1994

Tools: new page giving access to on-line analysis tools, such as BLAST, BLITZ, PROSITE search and amino acid composition analysis, and more to come in the future.

March 23, 1994

Added the list of restriction enzymes and methylases in SWISS-PROT top page.

March 22, 1994

The ExPASy WWW server has been upgraded to a SPARCServer 10/51. It should perform much faster now. If some features are not working, please tell us about.

March 18, 1994

The links to OMIM are now direct links to the OMIM hypertext server from GDB. Thanks to Keith Robison for informing me about it.

March 4, 1994

SWISS-2DPAGE: Added experimental Amino Acid Composition Similarity Search: you enter a protein's amino acid composition and the server will e-mail you the list of SWISS-PROT entries with similar compositions, sorted by decreasing similarity measure.

March 2, 1994

Added direct link to NCBI's BLAST Basic Local Alignment Search Tool (ExPASy and SWISS-PROT top pages).

March 1, 1994

Starting with release 28, SWISS-PROT keyword search will be performed on the main release as well as on the weekly updates.

In the SWISS-PROT page, added links to four additional active lists:

• Index of Escherichia coli K12 chromosomal entries in SWISS-PROT and their corresponding EcoGene cross-reference
• Index of Saccharomyces cerevisiae entries in SWISS-PROT and their corresponding gene designations
• Index of Caenorhabditis elegans entries in SWISS-PROT and their corresponding gene designations and WormPep cross-references
• Index of Dictyostelium discoideum entries in SWISS-PROT and their corresponding gene designations and DictyDB cross-references

February 23, 1994

Added two new reference 2-D PAGE maps: Macrophage Like Cell Line (U937) and Erythroleukemia Cell (ELC).

In a SWISS-2DPAGE entry, it is now possible to compute the theoretical pI and Mw of the protein.

February 14, 1994

Added SWISS-2DPAGE Map Selection: you select a 2-D PAGE reference gel, click on a spot and get information on the corresponding protein. See the SWISS-2DPAGE top page.

February 11, 1994

Added a new reference 2-D PAGE map of Cerebrospinal Fluid to SWISS-2DPAGE.

January 28, 1994

Added the bionet newsgroups.

January 25, 1994

Added an entry to SWISS-3DIMAGE images of crystallized proteins.

In SWISS-PROT entries which contain cross-references to PDB, added a cross-reference to SWISS-3DIMAGE. Try for example AAT_ECOLI.

January 24, 1994

Added full text search of the SWISS-PROT protein sequence database.

January 17, 1994

Added links to MEDLINE entries in SWISS-PROT, through NCBI's Entrez Server.

Added, in the SWISS-2DPAGE page, a link to the QUEST Protein Database Center.

December 1, 1993

Added a User Survey. Please help us inprove the server in participating to this survey.

Added a new reference 2-D PAGE map of Lymphoma to SWISS-2DPAGE.

November 23, 1993

Added link to BioBit 24, the BIO-NAUT Newsletter from November, 22, 1993, describing the World Wide Web.

November 18, 1993

Added links to the Maize Genome Database at Columbia, Missouri and to EMBnet Switzerland.

November 17, 1993

Added the list of overall Top Ten users in the ExPASy server Activity Reports page.

November 16, 1993

Added Images of crystallized proteins from this server.

Added links to Harvard Biological Laboratories, the Gene-Server at University of Houston, the EMBnet: Biocomputing in Europe, the biology servers index at USGS, Jackson Laboratory WWW server and Keith Robison's Molecular Biology WWW sampler.

October 12, 1993

Added a list of specialised documents to the SWISS-PROT top page, such as 7-transmembrane G-linked receptors, CD nomenclature for surface proteins of Human leucocytes and Vertebrate homeobox proteins. Some of these list give then direct access to corresponding SWISS-PROT entries.

October 8, 1993

Added links to the Caenorhabditis elegans and Mycobacterium databases at INRA (France).

Added a link to the ExPASy server activity reports.

October 4, 1993

Moved to the NCSA server.

September 28, 1993

Added the PDB Brookhaven Protein Data Bank of 3D structures. In SWISS-PROT, cross-references to PDB have now active links to the gopher server at Protein Data Bank. You may access the PDB entry or get the 3D image. Try for example the SWISS-PROT entry P00782.

September 27, 1993

Added the FlyBase database of genetic and molecular data for Drosophila. In SWISS-PROT and EMBL, cross-references to FLYBASE are now active links. Therefore, SWISS-PROT has now active links to SWISS-2DPAGE, EMBL, PROSITE, REBASE, OMIM and FLYBASE. EMBL has active links to SWISS-PROT and FlyBase.

September 23, 1993

Added a link to the National Institute of Health Genobase server to our top page.

September 21, 1993

Announced the ExPASy server and SWISS-2DPAGE release 0 to bionet.announce.

August 1, 1993

Installed the ExPASy molecular biology server, release 0, beta version.

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