SWISS-PROT

SWISS-PROT, which can be classified as a computer-annotated sequence repository. The issues of completeness and redundancy are also described, and examples of specialized protein sequence collections are given. 

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). 

PIR provides also some degree of crossreferencing to other biomolecu-lar databases by linking to the DDBJ/EMBL/GenBank nucleotide sequence databases, PDB, GDB, FlyBase, OMIM, SGD, and MGD. 

SWISS-PROT (Bairoch and Apweiler, 1999) is an annotated protein sequence database established in 1986 and maintained collaboratively by the Swiss Institute of Bioinformatics and the EMBL Outstation, The European Bioinformatics Institute (EBI). It strives to provide a high level of annotation, a minimal level of redundancy, a high level of 

A sample SWISS-PROT entry is shown in Fig. 1. The SWISS-PROT entries are made up of different line types, each of them beginning with a two-character line code indicative of the type of data stored in the line. There are 22 different line types in SWISS-PROT. Some line types may occur more than once in an entry, and some entries do not contain all line types. We will examine the entry in Fig. 1 and explain the different information found in the different lines  

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). 

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Swiss Prot EMBL and Swiss Institute of Bioinformatics protein sequence biblio., sub- stance, se- quence 120000 protein sequences, 44 mio amino adds journals, author submis- sions European Bioinformatics Institute free periodi- cally http //www.e- bi.ac.uk/swis- sprot/in- dex.html... 

Swiss-Prot, TrEMBL Annotated non-redundant protein sequence database, TrEMBL is a computer-annotated supplement to Swiss-Prot. TrEMBL contains the translations of all coding sequences present in the EMBL Nucleotide Sequence Database which are no yet integrated into Swiss-Prot... 

A Bairoch, R Apweiler. The SWISS-PROT protein sequence data bank and its supplement TrEMBL m 1999. Nucleic Acids Res 27 49-54, 1999. 

Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28 45-48... 

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/. 

Maintains the EMBL Nucleotide and SWISS-PROT databases as well as other databases.)... 

Upon alignment of 25 endo- and exo-polygalacturonases taken from the swiss.prot. database only one histidine appeared to be conserved throughout. The conserved histidine at position 223 in PGII was changed into alanine, a small apolar residue. 

Bacterial proteins from MALDI FTMS experiments are identifiable using the Swiss-Prot database.53 In order to identify any microorganism, it is neces-... 

Farriol-Mathis, N., Garavelli, J.S., Boeckmann, B., Duvaud, S., Gasteiger, S.E., Gateau, E., Veuthey, A.-L., Bairoch, A. (2004). Annotation of post-translational modifications in the Swiss-Prot knowledge base. Proteomics 4, 1537. 

P. diminuta 7 [320,368] N-terminal aminoacid sequence PIR Swiss-Prot Q51697 (a) and Q51698 ((3). S. Fetzner... 

The Swiss-Prot database is probably the most widely used protein database. It is maintained collaboratively by the European Bioinformatics Institute (EBI) and the Swiss Institute for Bioinformatics. It is relatively easy to access and search via the World Wide Web (Table 2.4). A sample entry for human insulin is provided in Figure 2.4. Additional information detailing such databases is available via the web addresses provided in Table 2.4 and in the bioinformatics publications listed at the end of this chapter. 

Figure 2.4 Sample entry for human insulin as present in the Swiss-Prot database. Refer to text for further details. Reproduced from the Swiss-Prot database on the Uniprot website htt //www.ebi.uniprot.org/...

GPCR and transporter protein information from SWISS-PROT has been imported as background data into the Arcadia database. This background information is used in Arcadia to simplify mutant submissions (wild-type proteins are already in the database and therefore do not have to be added by the user residue positions of the mutations... 

UniProt (http //www.expasy.uniprot.org), Universal Protein Resource. Created by joining the Swiss-Prot information, TrEMBL and PIR contains protein sequence and function. 

SWISS-PROT Coordinator, EMBL Outstation-The European Bioinformatics Institute. Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom... 

V. SWISS-PROT + TrEMBL A Complete and Nonredundant View on... 

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... 

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