Databases, protein sequence

The protein sequence database is also a text-numeric database with bibliographic links. It is the largest public domain protein sequence database. The current PIR-PSD release 75.04 (March, 2003) contains more than 280 000 entries of partial or complete protein sequences with information on functionalities of the protein, taxonomy (description of the biological source of the protein), sequence properties, experimental analyses, and bibliographic references. Queries can be started as a text-based search or a sequence similarity search. PIR-PSD contains annotated protein sequences with a superfamily/family classification. 

PIR-International Protein Sequence Database Redundant protein sequence database... 

Swiss-Prot, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

WC Barker, JS Garavelli, DH Haft, LT Hunt, CR Marzec, BC Orcutt, GY Snmvasarao, LSL Yeh, RS Ledley, HW Mewes, F Pfeiffer, A Tsugita. The PIR-International protein sequence database. Nucleic Acids Res 26 27-32, 1998. 

WR Pearson. Comparison of methods for searching protein sequence databases. Protein Sci 4 1145-1160, 1995. 

Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28 45-48... 

Henzel, W. J., Billeci, T. M., Stults, J. T., and Wong, S. C. (1993). Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 90, 5011-5015. 

W. J. Henzel, et al., Identifying Proteins from Two-Dimensional Gels by Molecular Mass Searching of Peptide Fragments in Protein Sequence Databases. Proc. Natl. Acad. Sci. U.S.A., 90, no. 11 (1993) 5011-5015. 

PIR (http //pir.georgetown.edu/), Protein Information Resource, located at Georgetown University Medical Center, which has provided the first international Protein Sequence Database. 

The protein sequence databases are the most comprehensive source of information on proteins. The goal of this chapter is to describe the different protein sequence databases available to researchers. It is necessary to distinguish between universal databases that cover proteins from all species and specialized data collections that store information about specific families or groups of proteins, or about the proteins of a specific organism. Two categories of universal protein sequence databases can be discerned simple archives of sequence data and annotated databases in which additional information has been added to the sequence record. The next section describes the Protein Information Resource (PIR), the oldest protein sequence database SWISS-PROT, an annotated universal sequence database and TrEMBL, the supplement of... 

Protein information resource (Barker et al., 1999) was established in 1984 by the National Biomedical Research Foundation (NBRF) as a successor to the original NBRF Protein Sequence Database, developed over 20 years by the late Margaret O. Dayhoff and published as the Atlas of Protein Sequence and Structure (Dayhoff et al., 1965 Dayhoff, 1979). Since 1988 the database has been maintained by PIR-Intemational, a collaboration between the NBRF, the Munich Information Center for Protein Sequences (MIPS), and the Japan International Protein Information Database (JIPID). 

SWISS-PROT (Bairoch and Apweiler, 1999) is an annotated protein sequence database established in 1986 and maintained collaboratively by the Swiss Institute of Bioinformatics and the EMBL Outstation, The European Bioinformatics Institute (EBI). It strives to provide a high level of annotation, a minimal level of redundancy, a high level of... 

PIR Protein sequence database of Protein Information Resource (PIR)... 

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. 

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 ... 

There are many specialized protein sequence databases. Some of them are quite small and contain only a handful of entries others are wider in scope and larger in size. This section describes three examples of specialized protein sequence databases. As this category of databases is quite changeable, any list provided here would soon be outdated. However, under the URL http //www.expasy.ch/alinks.html Proteins is a www document that lists information sources for molecular biologists that is continually update. 

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