SWISS-PROT protein sequence database

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 Protein Sequence Database, EMBL Data Library. D-6900 Heidelberg, Germany, and Amos Bairoch, Departement do Biochlmie Medicate, Centre Medical Undversitaire, [211 Geneva 4, Switzerland,... 

Expasy Swiss-Prot protein sequence and structure database http //www.expasy.ch/... 

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... 

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... 

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... 

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. 

SWISS-PROT (Annotated Protein Sequence Database)... 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

SWISS-PROT (Bairoch and Apweiler, 2000) is a protein sequence database that, from its inception in 1986, was produced collaboratively by the Department of Medical Biochemistry at the University of Geneva and the EMBL. The database is now maintained collaboratively by Swiss Institute of Bioinformatics (SIB) and EBI/EMBL. SWISS-PROT provides high-level annotations, including descriptions of the function of the protein and of the structure of its domains, its post-translational modifications, its variants, and so on. The database can be accessed from http //expasy.hcuge.ch/sprot/sprot-top.html or numerous mirror sites. In 1966, Translated EMBL (TrEMBL) was created as a computer-annotated supplement to SWISS-PROT (Bleasby et al, 1994). 

SWISS-PROT (Hofmann et al., 1999) is a curated protein sequence database maintained by the Swiss Institute of Bioinfornmatics and is a collaborative partner of EMBL. The database consists of SWISS-PROT and TrEMBL, which consists of entries in SWISS-PROT-like format derived from the translation of all CDS in the... 

UniProtKB/Swiss-Prot a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, posttranslational modifications, variants, etc.)... 

Introduction to Molecular Biology Databases. 1994-2004. R. Apweiler, R. Lopez, B. Marx, UniProt, SWISS-PROT, Switzerland. URL http //www.ebi.ac.uk/swissprot/Publications/ mbdl.html. Contents include bibliographic, taxonomy, nucleotide sequence, genetic, and protein sequence databases PIR, SWISS-PROT, and TrEMBL, and specialized protein, protein sequence, secondary protein, and structme databases. 

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). ... 

As mentioned in the introduction, there is now a considerable number of molecular biology and related databases available. While some are freely available, such as the DNA sequence collection EMBL [30] and GENBANK [18], others are only freely available to the academic community, such as the protein sequence database SWISS-PROT [15], and others are only available on subscription, such as the EST databases available from the company Incyte Genomics. Academics and pharmaceutical companies also have their own proprietary data which must be integrated into a system so that relationships with publicly available data can be found. 

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. 

Fig. 10.3 Human parvulins. Protein nomenclature is according to Fischer [3], The gene name and the molecular mass of the unprocessed proteins are shown in the brackets. In the second row, the accession number ofthe SWISS-PROT/ TREM BL database and an example of an alternative name ofthe protein is given. The amino acid residues that border the protein domains or functional modules are designated according to SWISS-PROT or Pfam databases. The parvulin domain is depicted in yellow. Signal sequence regions are shown as colorless boxes. WW, WW domain.

SWISS-PROT SWISS-PROT is an annotated protein sequence database maintained by the Swiss Institute of Bioinformatics and the EBI. The SWISS-... 

AACompSim, a variant of AACompIdent, performs a similar type of analysis, but, rather than using an experimentally derived amino acid composition as the basis for searches, the sequence of a SWISS-PROT protein is used instead (Wilkins et al., 1996). A theoretical pl and molecular weight are computed before computation of the difference scores using Compute pl/MW (see below). It has been documented that amino acid composition across species boundaries is well conserved (Cordwell et al., 1995) and that, by considering amino acid composition, investigators can detect weak similarities between proteins whose sequence identity falls below 25% (Ho-bohm and Sander, 1995). Thus the consideration of composition in addition to the ability to perform traditional database searches may provide additional insight into the relationships between proteins. 

In 2002, UniProt consortium (http //www.uniprot.org) was formed by uniting the SWISS-PROT -I- TrEMBL and PIR-PSD activities by maintaining a high-quality database that serves as a stable, comprehensive, fully classified and accurately annotated protein sequence knowledge base (Figure 16.2). The database offers extensive cross-references and querying interfaces fuUy accessible to the scientific community (Bairoch et al., 2005). The UniProt consortium produces three layers of protein sequence databases ... 

The expansion of protein sequence databases, e.g. TrEMBL, SWISS-PROT, NCBInr brought about by genome sequencing projects, dcCTeases the probability of obtaining an imequivocal protein idenffication by PME alone [118], More information like amino add sequence or amino acid composition increases the confidence in any protein identification. Lahm s group [118] defined three ways to reduce this problem ... 

The purpose of the molecular scanner is for the identification of proteins that were separated with a 2-DE gel. Therefore, for each scan point, the lists of peptide masses are submitted to the peptide mass fingerprint identification program Smartldent [51], which searches the protein sequence database SWISS-PROT and returns a list of matching proteins and their score. 

Swiss-Prot Highly annotated curated protein sequence database http //www.expasy.org/sprot... 

The increasing numbers of stored protein and nucleic acid sequences, and the recognition that functionally related proteins often had similar sequences, catalyzed the development of statistical techniques for sequence comparison which underlie many of the core bioinformatic methods used in proteomics today. Nucleic acid sequences are stored in three primary sequence databases - GenBank, the EMBL nucleotide sequence database, and the DNA database of Japan (DDBJ) - which exchange data every day. These databases also contain protein sequences that have been translated from DNA sequences. A dedicated protein sequence database, SWISS-PROT, was founded in 1986 and contains highly curated data concerning over 70 000 proteins. A related database, TrEMBL, contains automatic translations of the nucleotide sequences in the EMBL database and is not manually curated. 

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