SWISSPROT

In the biosciences, a database is a curated repository of raw data containing annotations, further analysis, and links to other databases. Examples of databases are the SWISSPROT database for annotated protein sequences or the FlyBase database of genetic and molecular data for Drosophila melanogaster. 

Swiss-Prot ia a curated databank of information on protein sequence, structure and function. It can be found under http //www.ebi.ac.uk/swissprot/. 

This is fundamental to the progress of genomics (and many other areas) of science. Generating data in a common exchangeable format, with a common lexicon of terms [47] in a single non-redundant location is a major goal. A number of examples exist, such as the DNA and protein sequence data in GenBank, EMBL or SwissProt [48-50]. 

SwissProt (http //www.expasy.org/sprot), database established by the Swiss Institute of Bioinformatics, provides protein sequences with high level of annotation. Highly integrated with other protein databases. All data are verified manually. 

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. 

Mascot (http //www.matrixscience.com/), a search engine that uses mass spectrometry data to identify peptides and proteins from primary sequence databases (MSDB, SwissProt, and others). 

Nuclear pore complex protein nu Accession number swissprot P52948... 

Pasquier, C., Promponas, V., Palaios, G., Hamodrakas, J., and Hamodrakas, S. (1999). A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database the PRED-TMR algorithm. Protein Eng. 12, 381-385. 

Additional data fields provide direct bibliographic links (using the Digital Object Identifier, DOI, format [14]) to PDF files for aU literature entries, and SwissProt [15] reference IDs for most targets. The SwissProt ID, in particular, can be challenging. 

Reference sequences. GPCRDB (http //www.gpcr.org/7tm/) and NCBI (http //www.ncbi.nlm.nih.gov/), SwissProt/ TrEMBL (http //www.expasy.org/sprot/). 

Lactobacillus acidophilus (strain R-26, heterodimeric enzyme, deoxyadenosine kinase/deoxguanosine kinase, i.e. dAK/dGK [19] SwissProt-ID U01881) [19]... 

Dictyostelium discoideum (gene MHCK A, myosin II heavy chain kinase A, SwissProt-ID P42527 [25]) [25]... 

Homo sapiens [4, 5] (SwissProt-ID Q8K4Q7) <4> Homo sapiens [4, 5] (SwissProt-ID Q8TCT0)... 

The sequence of the gene can be used to deduce the amino acid sequence of the protein encoded by the gene. The DNA and amino acid sequences can then be used to identify similar sequences in the large sequence databases such as GenBank (www.ncbi.nlm.nh.gov) or SWISSPROT (www.expasy.org). The chemical data obtained form the mutant combined with the sequence data from the gene that is defective in the mutant can then provide information on the function of the gene in the biosynthesis of a certain class of phenolic compounds. 

The ExPASy server (www.expasy.chl is one of the most useful servers, where almost any bioinforma tic tool can be found, together with useful links to other websites such as NCBI or EBI. The several access databases are descriptive, easy to follow, and up to date. Protein data bank searches with SwissProt or Trembl, as well as sequence alignments using either SimAlign (for two sequences) or ClustalW (for more than two protein sequences) can be started from ExPASy, to name just a few of the possibilities available. Access is also given to the Roche Applied Science Biochemical pathways where either keyword searches for particular enzymes or for metabolites can be performed, or entire metabolic pathways or sections thereof can be visualized. Proteomics evaluation is also available on ExPASy, which features free 2D-PAGE software called Melanie. 

SwissProt is, next to GenBank, the most important server for biologists, but it has a different philosophy behind it. In GenBank all entries are submitted by the authors themselves and underlie their authority in SwissProt all entries are screened by one person and his group, which makes entry acceptance slower (this speed has been increased by creating an accession buffer called trembl) but accuracy and efficacy is higher, and redundancy does not normally occur. 

Protein (amino acid) sequences are available from databases such as SwissProt/ Trembl or Protein Data Bank (PDB). Most useful is the ability of such databases to perform alignments, the comparison between different sequences. Simple alignment compares two sequences, multiple alignment more than two. 

Data gathering was through BLAST search in SwissProt (Peitsch, 1995,1996). 

Official gene name Other names/symbols Genbank accession number Unigene cluster Merops ID SwissProt ID... 

SwissProt is a relatively small but highly annotated database with minimal redundancy. NCBInr and MSDB are much larger, but have multiple entries for many proteins. Other search engines may have additional database choices, and in-house copies allow custom databases to be used. 

---