Swiss-Prot format

A typical TrEMBL entry is shown in Fig. 2. A TrEMBL entry looks much like a SWISS-PROT entry, because TrEMBL follows the SWISS-PROT format and conventions as closely as possible. A few differences affect the ID and DT lines. 

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). 

Figure 4.6. Swiss-Prot format for amino acid sequence of chicken egg-white lysozyme.

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). 

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. 

PIR (upper), Swiss-Prot (middle) and GenPept (lower) formats for amino acid sequence of chicken egg-white lysozyme are represented. Swiss-Prot format is the default format of EMBL/EBI and GenPept format is the default format adopted by GenBank (Entrez) and DDBJ (DBGet). Pasta format is shown in subsection 5.1.2. 

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 ... 

Fig. 4. Example of output from the seg program (Wootton, 1994). The seg program was run with default parameters on the SWISS-PROT sequence PSPDHUMAN. (A) Tree output format from seg. Lower case sequence on the left is low complexity, whereas the sequence on the right is high complexity. Note that only the regions between residues 13 and 47 and residues 152 and 375 are large enough to contain protein domains. (B) The second output from seg shows the regions of low complexity masked with Xs this sequence is ready for database searching.

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... 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

The annotated amino acid sequence files normally provide information concerning the sites and types for post-translational modifications and functions. These descriptions can be found from Features line(s) in all of the three sequence formats, namely, PIR, GenPept, and Swiss-Prot. The ExPASy Proteomics tools (http //www.expasy. ch/tools/) provide numerous links for such services. 

Once a set of entries which match the search terms has been retrieved, various operations can be performed on that set. The simplest is to view each whole entry in it, or to just view various fields from the entries. Predefined views, either part of the SRS package, or defined by the local SRS administrator, allow for the data to be presented in other formats. Figure 1.13 shows the default entry view of a whole SWISS-PROT entry. This looks considerably different to the text in the flat file, as shown in Figure 1.14, with the information easier to read. Either a pre-defined view of the entries can be used to view just some of the fields, or alternatively a view of the data... 

Increasing reproducibility of available separation techniques and sensitivity and affordability of mass spectrometers, as well as the desire and need to automate the identification process, have caused peptide mass fingerprinting and MS/MS sequencing to gain importance and to become the method of choice for many proteomics laboratories. Several tools are available to assist users in the interpretation of mass spectrometry data. Peptldent (http //www.expasy.org/tools/peptident.html) on the ExPASy server follows the concept of the other tools from the ExPASy proteomics suite, in that it takes into account annotation available in the SWISS-PROT/TrEMBL database, in particular as post-translational modifications and processing are concerned. The user can paste peptide masses (monoisotopic or average) into the Peptldent form, but peptide mass data can also be uploaded from a file on the user s local computer. Supported file formats are .pkm ... 

Example of a SWISS-PROT entry in its textual format. 

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. 

Sequences are submitted to PredictProtein either by sending an E-mail message or by using a Web front end. Several options are available for sequence submission the query sequences can be submitted as single-letter amino acid code or by its SWISS-PROT identifier. In addition, a multiple sequence alignment in PASTA format or as a PIR alignment can also be submitted for secondary structure prediction. 

Protein and DNA sequences can be inserted in separate blocks and this allows for more flexible designs (Fig. 6). The sequences can be entered as text or uploaded as files in multiple formats, including FASTA, GCG, GenBank, Swiss-Prot, and others. As many as 99... 

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