FASTA sequence format
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Description
One of the oldest and simplest sequence formats.
This file format can be parsed by the Bio::SeqIO system using the Bio::SeqIO::fasta module.
Examples
A sequence database with two protein sequences in FASTA format. The description line after the ">" is totally free-form, although applications often assume the first string after the ">" symbol is a sequence identifier of some sort. Traditionally the sequence lines are limited to a width of 60 characters.
>CATH_RAT MWTALPLLCAGAWLLSAGATAELTVNAIEKFHFTSWMKQHQKTYSSREYSHRLQVFANNWRKIQAHNQRN HTFKMGLNQFSDMSFAEIKHKYLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSCW TFSTTGALESAVAIASGKMMTLAEQQLVDCAQNFNNHGCQGGLPSQAFEYILYNKGIMGEDSYPYIGKNG QCKFNPEKAVAFVKNVVNITLNDEAAMVEAVALYNPVSFAFEVTEDFMMYKSGVYSSNSCHKTPDKVNHA VLAVGYGEQNGLLYWIVKNSWGSNWGNNGYFLIERGKNMCGLAACASYPIPQV >CATL_HUMAN MNPTLILAAFCLGIASATLTFDHSLEAQWTKWKAMHNRLYGMNEEGWRRAVWEKNMKMIELHNQEYREGK HSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYEAPRSVDWREKGYVTPVKNQGQCGSCWA FSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEES CKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLV VGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
An NCBI formatted sequence header which includes genBank-identifier number 142864, accession number M10040.1, and Locus name BACDNAE. This sequence was first submitted to the GenBank database as described by the gb prefixing the accession number. Other abbreviaions include emb for EMBL Database or pdb for PDB Database.
>gi|142864|gb|M10040.1|BACDNAE B.subtilis dnaE gene encoding DNA primase, complete cds GTACGACGGAGTGTTATAAGATGGGAAATCGGATACCAGATGAAATTGTGGATCAGGTGCAAAAGTCGGC AGATATCGTTGAAGTCATAGGTGATTATGTTCAATTAAAGAAGCAAGGCCGAAACTACTTTGGACTCTGT CCTTTTCATGGAGAAAGCACACCTTCGTTTTCCGTATCGCCCGACAAACAGATTTTTCATTGCTTTGGCT GCGGAGCGGGCGGCAATGTTTTCTCTTTTTTAAGGCAGATGGAAGGCTATTCTTTTGCCGAGTCGGTTTC TCACCTTGCTGACAAATACCAAATTGATTTTCCAGATGATATAACAGTCCATTCCGGAGCCCGGCCAGAG TCTTCTGGAGAACAAAAAATGGCTGAGGCACATGAGCTCCTGAAGAAATTTTACCATCATTTGTTAATAA ATACAAAAGAAGGTCAAGAGGCACTGGATTATCTGCTTTCTAGGGGCTTTACGAAAGAGCTGATTAATGA ATTTCAGATTGGCTATGCTCTTGATTCTTGGGACTTTATCACGAAATTCCTTGTAAAGAGGGGATTTAGT GAGGCGCAAATGGAAAAAGCGGGTCTCCTGATCAGACGCGAAGACGGAAGCGGATATTTCGACCGCTTCA GAAACCGTGTCATGTTTCCGATCCATGATCATCACGGGGCTGTTGTTGCTTTCTCAGGCAGGGCTCTTGG
Note
It is important to realise that there is no formal definition for the header line, so >CATL_HUMAN and >gi|7733636|ref|NP_887744 Gadget protein are both valid. NCBI has one format, Swissprot another, and so on. Therefore BioPerl has no guaranteed way of knowing where names, accessions, and particular identifiers are in the header line. There is some code which tries to guess accession_numbers out of these headers, when parsing BLAST reports but (see each_accession_number in Bio::Search::Hit::GenericHit).
File Extensions
There are no standard file extensions for FASTA formatted files. However, common ones are .fa and .fsa. NCBI distribute their genomic data in FASTA format using four different extensions: .fna for whole genomic DNA sequences, .faa for protein coding sequences (CDS), .ffn for the untranslated nucleotide sequences for each CDS, and .frn for nucleotide sequences of RNA related features.
