SWISS-PROT TrEMBL A Complete and Nonredundant View on Protein World

This section focuses on the use of SWISS-PROT + TrEMBL for sequence similarity searches. Searches in protein sequence databases have now become a standard research tool in the life sciences. To produce valuable results, the source databases should be comprehensive, nonredundant, well annotated, and up-to-date. However, lack of a single protein sequence database that satisfies all four criteria has previously forced users to perform searches across multiple databases to avoid incomplete results. This strategy normally produces complete but redundant results owing to different versions of the same sequence report in different databases. 

To improve this unsatisfying situation, many bioinformatics sites construct nonredundant databases from a number of component databases, or they use external nonredundant databases, e.g., OWL (Bleasby et al., 1994). Both strategies considerably improve the situation for the end user, but they require the time- and resource-consuming maintenance of multiple databases or the acceptance of a certain time lag between creation of an entry and its appearance in the nonredundant database. Furthermore, both strategies lead to a loss of information in the individual entry owing to the diversity of database formats. Whereas OWL preserves most information of an entry and some of its structure, the NRDB program requires a conversion of the component databases to FASTA format, which contains only one description line per entry. 

SP TR NRDB (or abbreviated SPTR) was created to overcome these limitations. SPTR provides a comprehensive, nonredundant and up-to-date protein sequence database with a high information content. The components are  

The weekly updated SWISS-PROT work release. This contains the last SWISS-PROT release as well as the new or updated entries. 

The weekly updated SP-TrEMBL work release. REM-TrEMBL is not included in SP TR NRDB because REM-TrEMBL contains the entries that will not be included in SWISS-PROT, e.g., synthetic sequences and pseudogenes. 

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V. Swiss-prot + TrEMBL A Complete and Nonredundant View on Protein World... 

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