SWISS-PROT protein sequence database linked databases

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

A variety of protein/DNA databases, such as GenBank, EMBL, NCBI, GenPept, Swiss-Prot, TrEMBL, PIR, OWL, IPI, and dbEST, are maintained by independent research groups for use by the public for proteome analysis. Databases have links to other databases and also provide vital information related to the identified proteins such as functions, any PTMs, domain and sites, 3D structures, homology to other proteins, associated diseases, sequence conflicts, and variants. 

Swiss-Prot and TrEMBL are the initial databases one would use to find information regarding the protein s sequence. Depending on the level of refinement and information provided for each sequence, data are deposited into either Swiss-Prot or TrEMBL. Because of the large number of sequences that are now determined from genomics alone, all sequences are first deposited into TrEMBL. Once the correct nomenclature, links to relevant databases, and significant comments are added, and after unnecessary information has been removed, the sequence is added to the Swiss-Prot database. The initial search for a sequence is typically performed on the information contained in these two databases. 

---