Database GENPEPT

To facilitate sequence efficiency, a variety of different primary sources are amalgamated to composite databases such as NRDB (PDB, Swiss-Prot, PIR, and GenPept), OWL (GenBank, PIR, Swiss-Prot, and NRL-3D), and MIPSX (PIR-MIPS, Swiss-Prot, NRL-3D, Kabat, and PseqlP). NRDB is built at the NCBI. The database is comprehensive and up-to-date however, it is not nonredundant but rather nonidentical. OWL (http //www.bioinf.man.ac.uk/dbbrowser/OWL/) is a non-... 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

The known functional sites are described in the FEATURE lines of the annotated sequence hies such as PIR, GenPept, and Swiss-Prot. The PRO SITE database (http //www.expasy.ch/sprot/prosite.html) consists of biologically significant patterns/prohles/signatures that may aid in identifying the query sequence to the known family of proteins (Hofmann et al., 2000). The database that is composed of two ascii (text) hies, PROSITE.dat and PROSITE.doc, can be downloaded using FTP from ExPASy (ftp //www.expasy.ch/databases/prosite/) or Swiss Institute for... 

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. 

Protein databases used to be from direct protein sequencing, but now they are made almost exclusively from the translation of ORFs (Open Reading Frames on DNA sequences). Both the European Bioinformatics Institute (EBI) and National Center for Biotechnology Information (NCBI) provide databases, TREMBL [15] and GENPEPT [19] respectively, which are automatic translations from the CDS features of the DNA in their nucleotide databases. This includes some automated annotation of the role which the protein plays. 

The National Center for Biotechnology Information (NCBI) presents their series of databases, GENBANK, GENPEPT, etc. on the web with a simple query form. The query form allows users to think about the data differently to how SRS works, with users searching for a DNA or protein sequence rather than searching a specific database. This allows scientists and occasional users to ask simple questions very quickly. However it is not possible... 

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