PIR Protein Sequence Database

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

The PIR Protein Sequence Database (Barker et al., 2001 Wu et al., 2002) developed at the National Biomedical Research Foundation (NBRF) has been maintained by PIR-International Protein Sequence Database (PSD), which is the largest publicly distributed and freely available protein sequence database. The consortium includes PIR at the NBRF, MIPS, and JIPID. PIR-International provides online access at http //pir.georgetown.edu to numerous sequence and auxiliary databases. These include PSD (annotated and classified protein sequences), PATCHX (sequences not yet in PSD), ARCHIVE (sequences as originally reported... 

LOX name for a lipoxygenase - names have been kept as much as possible in line with the names used for the LOXs from a species. For potato tuber LOX,a large number of highly similar sequences are available which have been numbered I a-1 g. Gene genomic sequences available in the EMBL nucleotide sequence database (release 49.0). DNA cDNA sequences available in the EMBL nucleotide sequence database (release 49.0) SWISS protein sequences available in the SWISSPROT protein sequence database (release 34.0). PIR protein sequences in the PIR protein sequence database (release 50,0). Remarks between brackets length In amino acid residues of partial sequences. Includes further names of specific clones, alternative names for a LOX used by the author. 

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... 

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. 

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). 

Selected entries from Methods in Enzymology [vol, page(s)] Databases and Resources Information services of European Bioinformatics Institute, 266, 3 TDB new databases for biological discovery, 266, 27 PIR-international protein sequence database, 266, 41 superfamily classification in PIR-international protein sequence database, 266, 59 gene classification artificial neural system, 266, 71 blocks database and its applications, 266, 88 indexing and using sequence databases, 266, 105 SRS information retrieval system for molecular biology data banks, 266, 114. 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

The Munich Information Center for Protein Sequences (MIPS) (Mewes et al., 2000) collects and processes sequence data for the PIR-International Protein Sequence Database project. Access to the database is provided through its Web server, http //www.mips.biochem.mpg.de/. The implementation of PrIAn (Protein Input and Annotation) data input has greatly increased database entries of PIR-International. 

The Protein Information Resources (PIR) (Wu et al., 2002) of NBRF in collaboration with MIPS and JIPID produces the annotated protein sequence database in the PIR-MIPS International Protein Sequence Database (PSD). The PSD is a comprehensive annotated and nonredundant protein sequence database. Its annotation includes concurrent cross-references to other sequence, structure, genomic and citatation databases, as well as functional descriptions and structural features. The PIR-International database is accessible at the PIR site, http //pir, georgetown.edu, and at the MIPS site, http //www.mips.biochem.mpg.de. 

Introduction to Molecular Biology Databases. 1994-2004. R. Apweiler, R. Lopez, B. Marx, UniProt, SWISS-PROT, Switzerland. URL http //www.ebi.ac.uk/swissprot/Publications/ mbdl.html. Contents include bibliographic, taxonomy, nucleotide sequence, genetic, and protein sequence databases PIR, SWISS-PROT, and TrEMBL, and specialized protein, protein sequence, secondary protein, and structme databases. 

The first resources for computer modeling of protein structure are the nucleic acid and protein sequence databases (see Table 6.1), curated by the European Molecular Biology Laboratory (EMBL) in Europe, the National Center for Biotechnology Information (GenBank at the NCBl) in the United States, and the DNA Database of Japan (DDBJ) in Japan. These databases are accessible via the Internet, and most likely one s own scientific institution maintains a local version, which is updated through CD-ROMs released quarterly. Perhaps the predominant protein sequence database is SWISS-PROT. - Others include the nonredundant protein sequence database (OWL) and the protein identification resource database (PIR). ... 

In 2002, UniProt consortium (http //www.uniprot.org) was formed by uniting the SWISS-PROT -I- TrEMBL and PIR-PSD activities by maintaining a high-quality database that serves as a stable, comprehensive, fully classified and accurately annotated protein sequence knowledge base (Figure 16.2). The database offers extensive cross-references and querying interfaces fuUy accessible to the scientific community (Bairoch et al., 2005). The UniProt consortium produces three layers of protein sequence databases ... 

PIR Protein information resource Protein sequence database http //pir.georgetown.edu/... 

Amino Acid Sequence Identity. The predicted amino acid sequences for the squalene-hopene and oxidosqualene-lanosterol cyclases have no significant similarities to sequences in protein sequence databases PIR 31 and SWISS-PROT 21 (40,42). However, when the predicted amino acid sequences of the cyclases are compared to one another, four regions of substantial similarity are observed. As... 

The SWISS-PROT database [36] release 40.44 (February, 2003) contains over 120 000 sequences of proteins with more than 44 million amino adds abstracted from about 100 000 references. Besides sequence data, bibHographical references, and taxonomy data, there are highly valuable annotations of information (e.g., protein function), a minimal level of redundancy, and a high level of integration with other databases (EMBL, PDB, PIR, etc.). The database was initiated in 1987 by a partnership between the Department of Medicinal Biochemistry of the University of Geneva, Switzerland, and the EMBL. Now SWISS-PROT is driven as a joint project of the EMBL and the Swiss Institute of Bioinformatics (SIB). 

PDB, NRL3D Protein Data Bank - protein structures (mostly fror X-ray crystallography). NRL3D is a derived sequence database in PIR format... 

Finally, knowledge of the peptide masses that resulted from the PIR conjugation provides information to identify the parent proteins from which they originated. Peptide mass and sequence databases now are sufficiently developed to provide rapid confirmation of protein-protein interaction partners. 

MSDB (ftp //ftp.ncbi.nih.gov/repository/MSDB), database created especially for MS applications. Contains nonidentical protein sequences obtained from other databases (PIR, TrEMBL, SwissProt). At http // www.matrixscience.com/help/seq db setup msdb.html, a guidebook for MSDB users can be found. 

This database provides both protein sequences which are deduced from DNA sequences registered in the European Molecular Biology Laboratory (EMBL) and those from the NBRF/PIR database. 

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