DATABANKS – a catalogue database of molecular biology databases

First, select ‘SRS World Wide’ from the SRS home page. This leads to a list of known public SRS servers. From here, users can choose to search DATABANKS – typically by databank name or description. More generally, any field present in the databank information pages, as well as site and server characteristics, can be used in a query.The results of the search show all the databanks that matched the search request and at which sites they are available. For convenience, the list of results offers direct links to their remote query forms, which feature a uniform interface that is both easy to use and flexible.Figure 1Figure 1 shows the result of a request for databanks named ‘ENZYME’. As in most cases, several servers maintain a copy of the database, and the list shows alternative sites. The number of indexed entries and the release number (where assigned by the server maintainers) help users to choose a nearby site that has a current version of the database.Figure 1The results of a query for databanks named ‘ENZYME’. The number of indexed entries and the release number (where assigned by the server maintainers) help users to choose a nearby server that offers a current version of the appropriate databank.View Large Image | Download PowerPoint SlideWhen searching for a particular database, users should first restrict the search to a subset of DATABANKS that includes only one site from each group of alternatives. (Currently, this representative site is chosen as the site that has the most extensive databank-information page.) This allows searching for databanks in two steps: (1) identification of the databases of interest; and (2) comparison of the sites at which they are offered (see Fig. 1Fig. 1).Consider a user who is interested in databases that offer sequence alignments, which hold information on well-characterized protein domains or families and can be used for functional assignments or phylogenetic examinations. Selecting the field ‘Description’ in the query form and asking for ‘sequence’ and ‘align’, yields a list of ∼60 databank copies; modified as shown in Fig. 2Fig. 2, however, the query fetches a more manageable list of only 15 representative databanks. In addition to general databases of protein domains or families [such as PFAM (Ref. 7xSonnhammer, E.L. et al. Nucleic Acids Res. 1998; 26: 320–322Crossref | PubMed | Scopus (437)See all ReferencesRef. 7), PRINTS (Ref. 8xAttwood, T.K., Beck, M.E., Bleasby, A.J., and Parry-Smith, D.J. Nucleic Acids Res. 1994; 24: 182–188Crossref | Scopus (22)See all ReferencesRef. 8) or PIRALN (Ref. 9xBarker, W.C. et al. Nucleic Acids Res. 1998; 26: 27–32Crossref | PubMed | Scopus (63)See all ReferencesRef. 9)], a user will also find specialized databases, such as HOVERGEN (vertebrates)10xDuret, L., Mouchiroud, D., and Gouy, M. Nucleic Acids Res. 1994; 22: 2360–2365Crossref | PubMed | Scopus (176)See all References10, AMmtDB (vertebrate mitochondria)11xLanave, C. et al. Nucleic Acids Res. 1999; 27: 134–137Crossref | PubMed | Scopus (7)See all References11, RDP (ribosomes)12xMaidak, B.L. et al. Nucleic Acids Res. 1997; 25: 109–111Crossref | PubMed | Scopus (695)See all References12, FSSP and HSSP (protein structure)13xHolm, L. et al. Protein Sci. 1992; 1: 1691–1698Crossref | PubMedSee all References, 14xSander, C. and Schneider, R. Proteins. 1991; 9: 56–68Crossref | PubMedSee all References, or TRANSFAC (transcription factors)15xHeinemeyer, T. et al. Nucleic Acids Res. 1998; 26: 362–367Crossref | PubMed | Scopus (1224)See all References15. The user can now browse the descriptions of the databases retrieved, and refine or broaden the search.Figure 2Query for databanks that have a description containing the terms ‘sequence’ and ‘align’. The second line of the query form requests that the results be restricted to one representative databank for each group of alternatives.View Large Image | Download PowerPoint SlideEach entry in DATABANKS contains a copy of the SRS databank-information page – as shown by the server it was collected from – and concludes with an overview of alternative sites. A typical entry is shown in Fig. 3Fig. 3. The overview provides direct links for remote queries to each of the sites. If a stable connection to a particular site could not be established, the site is moved to the end of the list of alternatives. In these cases, data from previous runs are used as backup. A record of when the backup was originally retrieved indicates whether it might be out of date.Figure 3A typical DATABANKS entry. The entry contains a copy of the respective remote SRS databank information page, which includes a description, references and links, as well as detailed documentation of database fields and indices. It concludes with a listing of alternative sites that offer ‘ENZYME’. Direct links to these sites and the remote query forms for ENZYME are provided. For users in the network vicinity of a particular DATABANKS server, the relative response times compiled by that server give a clue to the net distances to other sites (N/A indicates problems connecting at the specified time).View Large Image | Download PowerPoint SlideDATABANKS provides occasional users and experts alike with an up-to-date direct gateway into the ever-growing net of databanks, giving convenient access to a wide range of data and services.