Sequence databases/servers

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 Data Bank (PDB) is the primary structure database serving as the international repository for the processing and distribution of 3D structures of biomacromolecules (Bernstein et al, 1977). The database is operated by the Research Collaboratory for Structural Bioinformatics (RCSB) and is accessible from the primary RCSB site at http //www.rcsb.org/pdb/ (Berman et al., 2000). Most of the structure fold/motif/domain databases (Conte et al., 2000) and analysis servers (Brenner et al, 2000 Hofmann et al, 2000 Kelley et al., 2000 Shi et al., 2001) utilize 3D-structure information from PDB and sequence information from primary sequence databases. Some of these databases/analysis servers and their URL are listed in Table 12.3. 

The ProteinProspector Server (http //prospector.ucsf.edu) from the University of California San Francisco mass spectrometry facility. This suite of programs includes various tools for mining sequence databases in conjunction with mass spectrometry experiments, such as MS-Fit, MS-Tag, MS-Product and others. 

SWISS-PROT [25, http //www.expasy.org/sprot/] is a curated protein sequence database which provides a high level of annotation, such as the description of a protein s function, its domain structure, PTMs, conflicts between literature references and variants. It also provides a minimal level of redundancy, a high level of integration with other biomolecular databases, and an extensive external documentation. Created in 1986, it now includes more than 100 000 entries from more than 7000 different species. SWISS-PROT is available from more than 100 WWW servers world-wide and its main host is the ExPASy server. 

The ReHAB databases for viral genes at www.virology.ca are maintained and updated by the VBRC, allowing this data to be accessed by the general public. In addition to the use described here, ReHAB can also be set up as a standalone application utilizing a user s own database server, and with a user s own query sequences, but it should be noted that the system requirements are... 

Most algorithms require sets of sequences in FASTA format. Proteins are usually easily extracted directly from the available sequence databases. Genomic DNA is more problematic, because annotation of genes, promoters, transcriptional start sites, introns, exons, and other important features is not always reliable. Several web servers available to aid in extracting the relevant sequences for discovering regulatory elements in genomic DNA are shown in Table 1. 

Entrez searches can be performed using one of two Internet-based interfaces. The first is a client-server implementation known as NetEntrez. This makes a direct connection to an NCBI computer. Because the client software resides on the user s machine, it is up to the user to obtain, install and maintain the software, downloading periodic updates as new features are introduced. The second implementation is over the World Wide Web and is known as WWW Entrez or WebEntrez (simply referred to as Entrez). This option makes use of available Web browsers (e.g., Netscape or Explorer) to deliver search results to the desktop. The Web allows the user to navigate by clicking on selected words in an entry. Furthermore, the Web implementation allows for the ability to link to external data sources. While the Web version is formatted as sequential pages, the Network version uses a series of windows with faster speed. The NCBI databases are, by far the most often accessed by biochemists and some of their searchable fields include plain text, author name, journal title, accession number, identity name (e.g., gene name, protein name, chemical substance name), EC number, sequence database keyword and medical subject heading. 

All primary sequence databases provide tools for essential sequence analyses. Many servers are also available on the web to perform useful computation on DNA/RNA sequences and structures. These web servers (Table 15.9) provide an array of diverse computational genomic tools. 

SPTR is distributed in three files sprot.dat.Z, trembl.dat.Z, and trembl new.dat.Z. These files are, as indicated by their Z extension, Unix compress format files, which, when decompressed, produce ASCII files in SWISS-PROT format. Three others files are also available (sprot.fas.Z, trembl.fas.Z, and trembl new.fas.Z), which are compressed fasta format sequence files that are useful for building the databases used by FASTA, BLAST, and other sequence similarity search programs. These files should not be used for other purposes, because all annotation is lost when using this format. The SPTR files are stored in the directory /pub/databases/sp tr nrdb on the EBI FTP server (ftp.ebi.ac.uk) and in the directory /databases/sp tr nrdb on the ExPASyFTP server (ftp. expasy.ch). 

A nucleotide or peptide sequence is searched against the EST database using the BLAST (see BLAST server Karlin and Altschul, 1990 and 1993 Altschul et al., 1997) searching programs. 

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