FASTA format

In bioinformatics, FASTA format is a text-based format for representing either nucleic acid sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes.The format also allows for sequence names and comments to precede the sequences.

The simplicity of FASTA format makes it easy to manipulate and parse sequences using text-processing tools and scripting languages like Python and Perl.

Format

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (both are optional). There should be no space between the ">" and the first letter of the identifier. It is recommended that all lines of text be shorter than 80 characters. The sequence ends if another line starting with a ">" appears; this indicates the start of another sequence. A simple example of one sequence in FASTA format:

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX IENY

Format converters

FASTA files can be batch converted to or from MultiFASTA format using tools some of which are available as freeware. Tools are also available for batch conversion from chromatogram formats (ABI/SCF) to FASTA.

Header line

The header line, which begins with '>', gives a name and/or a unique identifier for the sequence, and often lots of other information too. Many different sequence databases use standardized headers, which helps when automatically extracting information from the header. The header line may contain more than one header, separated by a ^A (Control-A) character (as in [ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz] ).

In the original Pearson FASTA format, one or more comments, distinguished by a semi-colon at the beginning of the line, may occur after the header. Most databases and bioinformatics applications do not recognize these comments and follow [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml the NCBI FASTA specification] . An example of a multiple sequence FASTA file follows:

>SEQUENCE_1MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEGLVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHKIPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTLMGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL>SEQUENCE_2SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQIATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH

equence representation

After the header line and comments, one or more lines may follow describing the sequence: each line of a sequence should have fewer than 80 characters. Sequences may be protein sequences or nucleic acid sequences, and they can contain gaps or alignment characters (see sequence alignment). Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap character; and in amino acid sequences, U and * are acceptable letters (see below). Numerical digits are not allowed but are used in some databases to indicate the position in the sequence.

The nucleic acid codes supported are:

Example Header Block:

#Dbcomponent=1
#Name=UniProt_SwissProt
#PrimaryIdentifierType=sp_ac
#Version=52.3
#ReleaseDate=20070425
#NumberOfEntries=248942
#Sequence_type=Protein_sequence

#Dbcomponent=2
#Name=ENSEMBL
#PrimaryIdentifierType=sp_ac
#Version=12.45.3.2
#ReleaseDate=20070425
#NumberOfEntries=1234567
#Sequence_type=Protein_sequence

equence header line

Example Protein Entry:

>sp_ac|P02769_WOSIG0 ID=ALBU_BOVIN DE="Serum albumin precursor (Allergen Bos d 6) (BSA)" NCBITAXID=9913 MODRES=(1|Acetyl) VARIANT=(196|A|T) LENGTH=589RGVFRRDTHKSEIAHRFKDLGEEHFKGLVLIAFSQYLQQCPFDEHVKLVNELTEFAKTCVADESHAGCEKSLHTLFGDELCKVASLRETYGDMADCCEKQEPERNECFLSHKDDSPDLPKLKPDPNTLCDEFKADEKKFWGKYLYEIARRHPYFYAPELLYYANKYNGVFQECCQAEDKGACLLPKIETMREKVLASSARQRLRCASIQKFGERALKAWSVARLSQKFPKAEFVEVTKLVTDLTKVHKECCHGDLLECADDRADLAKYICDNQDTISSKLKECCDKPLLEKSHCIAEVEKDAIPENLPPLTADFAEDKDVCKNYQEAKDAFLGSFLYEYSRRHPEYAVSVLLRLAKEYEATLEECCAKDDPHACYSTVFDKLKHLVDEPQNLIKQNCDQFEKLGEYGFQNALIVRYTRKVPQVSTPTLVEVSRSLGKVGTRCCTKPESERMPCTEDYLSLILNRLCVLHEKTPVSEKVTKCCTESLVNRRPCFSALTPDETYVPKAFDEKLFTFHADICTLPDTEKQIKKQTALVELLKHKPKATEEQLKTVMENFVAFVDKCCAADDKEACFAVEGPKLVVSTQTALA

ee also

*FASTA Search
*Stockholm format

External links

* [http://www.proteomecommons.org/data/fasta/hupo_standard.jsp HUPO-PSI Standard FASTA Format] describes another FASTA format as put forward by the Human Proteome Organisation's Proteomics Standards Initiative.
* [http://iubio.bio.indiana.edu/soft/molbio/readseq/ Readseq] for converting sequence formats to FASTA - Not updated since 1999. Needs Java.
* [http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi Readseq online at IUBio] -- [http://searchlauncher.bcm.tmc.edu/seq-util/readseq.html Readseq online at BCM]
* [http://www.bugaco.com/bioinf/ Nexus to Fasta converter] - Needs Java
* [http://gp2fasta.ovh.org/ GenBank to Fasta conventer] - Poorly documented.