What is Swiss-Shop ?

Purpose of Swiss-Shop
New Protein Sequences, which are added to the SWISS-PROT database on a weekly basis can be scanned following a user-defined query. The searches are performed on the current non-cumulative weekly additions only. This will allow researchers to be aware of new protein sequences, related to their interests, before the actual database release. All Results will be returned to the client via E-mail.

Purpose of Swiss-Shop

New Protein Sequences, which are added to the SWISS-PROT database on a weekly basis can be scanned following a user-defined query. The searches are performed on the current non-cumulative weekly additions only. This will allow researchers to be aware of new protein sequences, related to their interests, before the actual database release.

All Results will be returned to the client via E-mail.

Submitting Requests to Swiss-Shop

The only way to submit requests to Swiss-Shop is via the WWW interface, where you find a submission form to clearly formulate your request.
You MUST complete the fields E-mail address and Title of your query.
You may choose between Sequence/Pattern or KeyWord based searches.

SEQUENCE: Submit either a SWISS-PROT entry name (ID) or accession number (AC) or paste a raw sequence into the appropriate window. If you enter a SWISS-PROT ID or AC number or your own protein sequence, Swiss-Shop will perform, at each weekly update of SWISS-PROT, a BLAST alignment of your sequence against the sequences that have been added in SWISS-PROT since the last weekly update. You will receive an email message containing a list of new sequences thus found to be similar to your specified protein (with a probability P(N) below a user-specified threshold that the alignment is real and not random).
OR
PATTERN: Submit a protein pattern in PROSITE format. If you enter a PROSITE ID or AC or your own pattern in PROSITE format, 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 SWISS-PROT entries matching your pattern.
OR
KEYWORD: You may search entries using Authors (RA lines of SWISS-PROT), Taxonomy (OS,OG and OC lines) or Keywords (DE,CC and KW lines), Cross-references to other databases (DR) and terms appearing on the feature (FT) lines of SWISS-PROT.
NOTE: Horizontally, multiple query words are considered as logical "OR", while vertically they are considered as logical "AND".
Example:

Swiss-Shop example

Submitting Requests to Swiss-Shop
The only way to submit requests to Swiss-Shop is via the WWW interface, where you find a submission form to clearly formulate your request. You MUST complete the fields E-mail address and Title of your query. You may choose between Sequence/Pattern or KeyWord based searches. SEQUENCE: Submit either a SWISS-PROT entry name (ID) or accession number (AC) or paste a raw sequence into the appropriate window. If you enter a SWISS-PROT ID or AC number or your own protein sequence, Swiss-Shop will perform, at each weekly update of SWISS-PROT, a BLAST alignment of your sequence against the sequences that have been added in SWISS-PROT since the last weekly update. You will receive an email message containing a list of new sequences thus found to be similar to your specified protein (with a probability P(N) below a user-specified threshold that the alignment is real and not random). OR PATTERN: Submit a protein pattern in PROSITE format. If you enter a PROSITE ID or AC or your own pattern in PROSITE format, 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 SWISS-PROT entries matching your pattern. OR KEYWORD: You may search entries using Authors (RA lines of SWISS-PROT), Taxonomy (OS,OG and OC lines) or Keywords (DE,CC and KW lines), Cross-references to other databases (DR) and terms appearing on the feature (FT) lines of SWISS-PROT. NOTE: Horizontally, multiple query words are considered as logical "OR", while vertically they are considered as logical "AND". Example:

Performing the analyses included in the Swiss-Shop services on the FULL SWISS-PROT/TrEMBL database
If you wish to perform the analyses we offer in Swiss-Shop not only on the weekly updates, but on the complete SWISS-PROT/TrEMBL database, please choose one of the following locations:

Sequence-based searches
Use one of the alignment tools (e.g. BLAST) in the section 'similarity searches' of the ExPASy tools page for what is called 'sequence-based search' in Swiss-Shop.

Pattern-based searches
Use the ScanProsite or ProfileScan tools (also accessible from the ExPASy tools page, section 'Pattern and profile searches') for what is called 'pattern-based search' in Swiss-Shop.

Keyword-based searches
You can go to the SWISS-PROT top page and search the database using the 'direct access' methods there, or follow the link to the Sequence Retrieval System SRS.

Related services
Sequence alerting system at EMBL - daily searches in several databases for news of homologues of "your" sequence

Performing the analyses included in the Swiss-Shop services on the FULL SWISS-PROT/TrEMBL database
If you wish to perform the analyses we offer in Swiss-Shop not only on the weekly updates, but on the complete SWISS-PROT/TrEMBL database, please choose one of the following locations: Sequence-based searches Use one of the alignment tools (e.g. BLAST) in the section 'similarity searches' of the ExPASy tools page for what is called 'sequence-based search' in Swiss-Shop. Pattern-based searches Use the ScanProsite or ProfileScan tools (also accessible from the ExPASy tools page, section 'Pattern and profile searches') for what is called 'pattern-based search' in Swiss-Shop. Keyword-based searches You can go to the SWISS-PROT top page and search the database using the 'direct access' methods there, or follow the link to the Sequence Retrieval System SRS.

Related services
Sequence alerting system at EMBL - daily searches in several databases for news of homologues of "your" sequence

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Last modified 20/Sep/2000 by ELG

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