EMBL/Swiss-Prot

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). 

Nucleic acid and protein sequence analysis, including secondary structure prediction. GenBank, EMBL, SWISS-PROT, PIR, PROSITE, NASITE, and Vector-Bank databases on CD-ROM. Macintosh. PC/GENE for sequence analysis on PCs. IntelliGenetics Suite Sequence Analysis Software and GENESEQ database with patented protein and nucleic acid sequences. Sun and VAX. 

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). 

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... 

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

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

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... 

The next lines, the OS (Organism Species) and OC (Organism Classification), describe the species from which the protein has been derived. The OS line shows the scientific name of the organism and, if existing, the common English name. The OC lines give the taxonomic tree. SWISS-PROT, as well as the DDBJ/EMBL/GenBank nucleotide sequence databases, uses the NCBI taxonomy to standardize the taxonomies of the molecular sequence databases. 

CC This SWISS-PROT entry is copyright. It is produced CC through a Collaboration between the Swiss Institute of CC Bioinformatics and the EMBL outstation - the European CC Bioinformatics Institute. There are no restrictions on CC its use by non-profit institutions as long as its content CC is in no way modified and this statement is not removed. 

The DR lines link SWISS-PROT to other biomolecular databases. SWISS-PROT is currently linked to 29 different databases. The preceding example shows links to 19 different entries in 6 different databases. The cross references allow users to navigate to linked databases to retrieve part or all of the related information. The format of a DR line, except for cross references to PROSITE (Hofmann et al., 1999), Pfam (Bateman et al., 1999), and the EMBL nucleotide sequence databases (Stoesser et al., 1999), is the following ... 

The version number changes only when the protein sequence coded by the CDS changes, and the stable part remains unchanged. The "STATUS IDENTIFIER" provides information about the relationship between the sequence in the SWISS-PROT entry and the CDS in the corresponding EMBL entry. 

The SWISS-PROT and TrEMBL ID lines differ in the first two parts of the ID line. The first part is the entry name "ANP NOTCO" in the case of the SWISS-PROT example and "Q12757" in the TrEMBL example. The entry name used in all SP-TrEMBL entries is always the same as the accession number of the entry. The entry name used in REM-TrEMBL is the Protein ID tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. To the right of the entry name you will find either "preliminary" (in the TrEMBL entry) or STANDARD (in the SWISS-PROT entry). The data class used in TrEMBL is always PRELIMINARY. That means that the data are thoroughly checked by a computer,... 

The EMBL keywords are included in the TrEMBLnew entry, but only when they match a subset of SWISS-PROT keywords that have the same meaning. Another condition is that the EMBL entry has just one CDS so that no ambiguity is possible. Some extra keywords derived from the features and description lines are added. A subset of SWISS-PROT features can be derived from the EMBL entry features. These are ... 

The entries from the composite divisions of the EMBL database (HTG, STS, EST, and UNC) are now added to their relative taxonomic TrEMBLnew divisions. Then all hies are searched for entries that have recently been added to SWISS-PROT or TrEMBL and are thus missing a /dbxref = SWISS-PROT or a /dbxref = SPTREMBL qualifier in EMBL. These entries are removed. The entries put in the hies patent.dat, immuno.dat, smalls.dat, synthetic.dat and pseudo.dat are now already at the end of their production line. They are new entries in REM-TrEMBL (REMaining TrEMBL), which contains the entries (about 44,000 in release 10) that will not be included in SWISS-PROT. This section is organized in hve subsections ... 

Each SWISS-PROT entry consists of general information about the entry (e.g., entry name and date, accession number), Name and origin of the protein (e.g., protein name, EC number and biological origin), References, Comments (e.g., catalytic activity, cofactor, subuit structure, subcellular location and family class, etc.), Cross-reference (EMBL, PIR, PDB, Pfam, ProSite, ProDom, ProtoMap, etc.), Keywords, Features (e.g., active site, binding site, modification, secondary structures, etc.), and Sequence information (amino acid sequence in Swiss-Prot format, Chapter 4). 

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... 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

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,... 

UniProtKB/TrEMBL a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot. 

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. 

Accession numbers starting with P-Q are from the Swiss-Prot databank, others from the EMBL/GenBank ( crystal structure reference). 

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. 

Databanks such as SWISS-PROT and EMBL are also including variation information in their annotations. 

On the one hand, genome sequencing projects are generating a dramatically increasing number of sequences to be incorporated in SWISS-PROT. On the other, the number of annotators, who screen literature and sequence databases to populate SWISS-PROT with the high quality annotations, is limited. However, despite the increase in available raw sequence data it was not judged appropriate to automatically populate SWISS-PROT with data of lower quality standards. This is where TrEMBL (Translation of EMBL... 

Nucleotide Sequence Database [26]) steps in. TrEMBL was created in 1996 and consists of computer-annotated entries in SWISS-PROT-like format. It is populated by protein sequences translated from the coding sequences (CDS) in EMBL and is a supplement to SWISS-PROT. In a way, it can be considered as a preliminary section of SWISS-PROT indeed, once the manual annotation is performed, the entries move on to SWISS-PROT. 

Within the computer science community, regular expressions may be considered a standard [3]. The Open Group has an online standard on this topic (table 2.4). They are working to unify various approaches, including Unix and Perl 5 regular expressions. On the life sciences side, the controlled vocabularies provided by DDBJ/EMBL/GenBank and Swiss-Prot features are de facto standards. 

---