FASTA format
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In bioinformatics, FASTA format is a file format used to exchange information between genetic sequence databases. Its format looks like this:
>SEQUENCE_1 ;comment line 1 (optional) MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 ;comment line 1 (optional) ;comment line 2 (optional) SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
It consists of a header line (beginning with a '>') which gives a name and/or a unique identifier for the sequence, and often lots of other information too. Many different sequence databases use standarized headers, which helps when automatically extracting information from the header. Often the first 'word' of the header is a unique identifier for the protein sequence.
After the header line, one or more comments, distinguished by a semi-colon at the beginning of the line, may occur. Most databases and bioinformatics applications do not recognize these comments so their use is discouraged, but they are part of the official format.
After the header line and comments, one or more sequence lines may follow. Sequences may be protein sequences or DNA sequences, they must be shorther than 80 characters and can contain gaps or alignment characters (see sequence alignment).
FASTA format files often have file extensions like .fa, .mpfa or .fsa (and probably many more!).
The simple format of FASTA files makes them easy to manipulate using text processing tools and scripting languages like Perl.
The NCBI have gone so far as to define a standard for their fasta header (although generally this is a bit messy). The formatdb man page has this to say on the subject of FASTA format databases, "formatdb will automatically parse the SeqID and create indexes, but the database identifiers in the FASTA definition line must follow the conventions of the FASTA Defline Format."
However they do not give a difinitive description of the FASTA defline format, an attempt to create such a format is given below.
GenBank gi|gi-number|gb|accession|locus EMBL Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
See also
External links
- Sequence Formats (http://ngfnblast.gbf.de/docs/input_formats.html)