Nonredundant protein sequence database

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. 

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). ... 

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 ... 

Figure 6.13 BLAST search results. Part of the results from a BLAST search of the nonredundant (nr) protein sequence database with the use of the sequence of ribose-5-phosphate isomerase (also called phosphopentose isomerase, pp. 572 and S81) from coli as a query. Among the 268 sequences found is the orthologous sequence from human beings, and the alignment between these sequences is shown (highlighted in yellow). The number of sequences with this level of similarity expected to be in the database by chance is 2 X 10 as shown by the E value (highlighted in red). Because this value is much less than 1, the observed sequence alignment is highly significant.

The UniProt Reference databases (UniRel) provide nonredundant data collections based on the UniProtKB and UniParc, in order to obtain complete coverage of sequence space at several resolutions. UniRef databases (sequence collections clustered by sequence identity, for performing faster homology searches) are created as representative protein sequence databases witli high information content. 

The databases listed in Table 8.2 are maintained by independent research groups and can be accessed through the Internet. Some of these databases are nucleotide databases, and some protein databases that have been translated from the nucleotide databases. They are updated frequently and contain comprehensive lists of protein and nucleotide sequences. The choice of a particular database is dictated by the extensiveness of sequence entries, low redundancy rate, low error rate, and a high degree of annotation. A custom-made database can be assembled into a composite nonredundant database by including entries from all protein databases and translated-nucleotide databases (into protein sequences) and removing any duplicate entries. 

The PepSeq program of Micromass s ProteinLynx software package was used for de novo analysis of the sequence (MS/MS) data. MS-Pattern of ProteinProspectror55 used the sequence tag determined from PepSeq to search the nonredundant database of the National Center for Biotechnology Information (NCBI) for protein identification. 

Peptide identified from CID-MS/MS shown in Fig. 4D (major sequence-related ions of the peptide are indicated in the spectrum) by BioWorks (version 3.2, Thermo Fisher, San Jose, CA, USA) using the National Center for Biotechnology Information (NCBI) nonredundant (nr) protein database with rat (R. norvegicus) selected in the species option of the program... 

---