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http://www.biotech.ist.unige.it/interlab/mpdb.html
Marra, D.1, Malusa, F.1, Facchiano, A.2, Romano, P.1
1Biotechnology Department, National Cancer Research Institute, Genova, Italy
2Istituto di Scienze dell'Alimentazione CNR, Avellino, Italy
Contact paolo@ist.unige.it
The Molecular Probe Data Base (MPDB) was set up in 1992 with the objective of allowing researchers to retrieve information on molecular probes and synthetic oligonucleotides that had proven useful in real experimental conditions. MPDB includes information on synthetic oligos that can either be used as probes or as primers. Information was derived from scientific literature. Only oligonucleotides of length lesser than 100 bp were considered. More than 4000 entries are stored in MPDB. Oligonucleotides are described on the basis of: name, oligo type (primer, probe, antisense), nucleotidic sequence, amino acid sequence (if part of a coding region), target gene and related infos (localization within the gene and recognized variants or specificities), applications, methods, technical notes, complementary primer (if used for PCR), primers for amplification (if probe), bibliographic references. Integration with other molecular biology databases is ensured with links to: i) EMBL Data Library, through the Target Gene accession number, ii) PubMed, through the PubMed PMID identifier, iii) HSAGENES database, through the HUGO code of the target gene. Further links are being implemented including those to GDB and GeneCard. MPDB contents are particularly adequate for the setting up of internal links, links that connect two different entries of the same database: pair of primers are used for PCR methods, probes can be a result of a PCR amplification and pairs of primers can be used to amplify a probe. The following links were defined: i) between primers conjunctly used for PCR, ii) between a primer and the probes that it can amply, iii) between a probe and the primers that can be used for its amplification. These links have been actually set up in MPDB. Through an SRS search, it is possible to search for a specific probe and retrieve the information about the primers that are needed for its amplification. This can either be done by performing an SRS link operation or by using the HTML links that are included in the display of the results. MPDB is currently managed by using MySQL, an "open source" relational database, while searches are only allowed through implementations of the SRS integration software. MPDB data structure includes few free texts: the majority of the information is encoded and managed through controlled vocabularies. Information is often represented with one of a few items taken from the vocabularies. This is true for the applications and the methods where the SRS index includes the entire expressions that define items of the controlled vocabulary. E.g., "apolipoprotein deficit" is not indexed by using the keys "apolipoprotein" and "deficit", but under the unique key "apolipoprotein deficit". MPDB is currently available for searching through SRS implementations at the National Cancer Research Institute, Genoa, IT, http://srs.biotech.ist.unige.it/ (SRS 5) and http://srs6.biotech.ist.unige.it (SRS 6), and at the Research Center of Computational and Biotechnological Sciences, Naples, IT) http://crisceb.unina2.it/srs5/ (SRS5 5). MPDB is referenced as MOLPROBE. MPDB can easily be implemented in every SRS site. The data file and the related syntax files are available for downloading at: ftp://ftp.biotech.ist.unige.it/pub/MPDB/ .
A general revision of included information and data structure has recently being carried out, by comparing MPDB with other databases such as EBI primers, HGMP Primer catalogue and OPD. A new web site including the implementation of MPDB with SRS 6 is now available. Moreover, the new structure and syntax files that are needed to install MPDB in an SRS 6 site have been created and are available for download.
Category Varied Biomedical Content
