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.

• text based

• nucleic acid sequences
• peptide sequences

• begins with a single-line description, followed by lines of sequence data
• 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

simple examples:

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

example of a multiple sequence FASTA file:

>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH

• begins with “>”
• word following is the identifier and/or name of the sequence (optional)
• rest of the line is the description (optional)
• no space between the “>” and the first letter of the identifier
• header line may contain more than one header separated by a ^A (Control-A) character

• Sequence identifiers:
  • Many different sequence databases use standardized headers, which helps when automatically extracting information from the header
  • NCBI defined a standard for the unique identifier
  • they do not give a definitive description of the FASTA defline format, an attempt to create such a format:

    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

• After the header line and comments
• each line of a sequence should have fewer than 80 characters
• Sequences may be protein sequences or nucleic acid sequences
• can contain gaps or alignment characters
• 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
  • in amino acid sequences: U and * are acceptable letters
• Numerical digits are not allowed but are used in some databases to indicate the position in the sequence

The nucleic acid codes supported are:

The amino acid codes supported are: