FASTA format

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In bioinformatics, FASTA format is a text-based format for representing either nucleotide sequences or peptide sequences, in which nucleotides or amino acids are represented using single-letter codes. The format also allows for sequence names and comments to precede the sequences. The format originates from the FASTA software package, but has now become a standard in the field of bioinformatics.

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

Format[edit]

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|31563518|ref|NP_852610.1| microtubule-associated proteins 1A/1B light chain 3A isoform b [Homo sapiens]
   MKMRFFSSPCGKAAVDPADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKI
   IRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETFGF

History[edit]

The original FASTA/Pearson format is described in the documentation for the FASTA suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc or fastaVN.me—where VN is the Version Number).

A sequence in FASTA format is represented as a series of lines, each of which should be no longer than 120 characters and usually do not exceed 80 characters. This probably was to allow for preallocation of fixed line sizes in software: at the time most users relied on DEC VT (or compatible) terminals which could display 80 or 132 characters per line. Most people preferred the bigger font in 80-character modes and so it became the recommended fashion to use 80 characters or less (often 70) in FASTA lines. Also, the width of a standard printed page is 70 to 80 characters (depending on the font).

The first line in a FASTA file starts either with a ">" (greater-than) symbol or, less frequently, a ";" (semicolon) and was taken as a comment. Subsequent lines starting with a semicolon would be ignored by software. Since the only comment used was the first, it quickly became used to hold a summary description of the sequence, often starting with a unique library accession number, and with time it has become commonplace use to always use ">" for the first line and to not use ";" comments (which would otherwise be ignored).

Following the initial line (used for a unique description of the sequence) is the actual sequence itself in standard one-letter code. Anything other than a valid code would be ignored (including spaces, tabulators, asterisks, etc...). Originally it was also common to end the sequence with an "*" (asterisk) character (in analogy with use in PIR formatted sequences) and, for the same reason, to leave a blank line between the description and the sequence.

A few sample sequences:

   ;LCBO - Prolactin precursor - Bovine
   ; a sample sequence in FASTA format
   MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
   EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
   VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
   ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
   >MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
   ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
   FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
   DIDGDGQVNYEEFVQMMTAK*
   >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
   LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
   EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
   LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
   GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
   IENY

A multiple sequence FASTA format would be obtained by concatenating several single sequence FASTA files. This does not imply a contradiction with the format as only the first line in a FASTA file may start with a ";" or ">", hence forcing all subsequent sequences to start with a ">" in order to be taken as different ones (and further forcing the exclusive reservation of ">" for the sequence definition line). Thus, the examples above may as well be taken as a multisequence file if taken together.

Description line[edit]

The description line (defline) or header line, which begins with '>', gives a name and/or a unique identifier for the sequence, and may also contain additional information. In a deprecated practice, the header line sometimes contained more than one header, separated by a ^A (Control-A) character.

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. Some databases and bioinformatics applications do not recognize these comments and follow the NCBI FASTA specification. An example of a multiple sequence FASTA file follows:

>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH

Sequence representation[edit]

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:[1][2]

Nucleic Acid Code Meaning Mnemonic
A A Adenine
C C Cytosine
G G Guanine
T T Thymine
U U Uracil
R A or G puRine
Y C, T or U pYrimidines
K G, T or U bases which are Ketones
M A or C bases with aMino groups
S C or G Strong interaction
W A, T or U Weak interaction
B not A (i.e. C, G, T or U) B comes after A
D not C (i.e. A, G, T or U) D comes after C
H not G (i.e., A, C, T or U) H comes after G
V neither T nor U (i.e. A, C or G) V comes after U
N A C G T U Nucleic acid
X masked
- gap of indeterminate length

The codes supported (24 amino acids and 3 special codes) are:

Amino Acid Code Meaning
A Alanine
B Aspartic acid or Asparagine
C Cysteine
D Aspartic acid
E Glutamic acid
F Phenylalanine
G Glycine
H Histidine
I Isoleucine
J Leucine or Isoleucine
K Lysine
L Leucine
M Methionine
N Asparagine
O Pyrrolysine
P Proline
Q Glutamine
R Arginine
S Serine
T Threonine
U Selenocysteine
V Valine
W Tryptophan
Y Tyrosine
Z Glutamic acid or Glutamine
X any
* translation stop
- gap of indeterminate length

Sequence identifiers[edit]

The NCBI defined a standard for the unique identifier used for the sequence (SeqID) in the header line. The formatdb man page has this to say on the subject: "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."

The following list describes the NCBI FASTA defline format (see "The NCBI Handbook", Chapter 16, The BLAST Sequence Analysis Tool.).

 GenBank                           gb|accession|locus
 EMBL Data Library                 emb|accession|locus
 DDBJ, DNA Database of Japan       dbj|accession|locus
 NBRF PIR                          pir||entry
 Protein Research Foundation       prf||name
 SWISS-PROT                        sp|accession|entry name
 Brookhaven Protein Data Bank      pdb|entry|chain
 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

The vertical bars in the above list are not separators in the sense of the Backus-Naur form, but are part of the format. Multiple identifiers can be concatenated, again, separated by |s.

File extension[edit]

There is no standard file extension for a text file containing FASTA formatted sequences. The table below shows each extension and its respective meaning.

Extension Meaning Notes
fasta (.fas) generic fasta Any generic fasta file. Other extensions can be fa, seq, fsa
fna fasta nucleic acid Used to generically specify nucleic acids.
ffn FASTA nucleotide coding regions Contains coding regions for a genome.
faa fasta amino acid Contains amino acids. A multiple protein fasta file can have the more specific extension mpfa.
frn FASTA non-coding RNA Contains non-coding RNA regions for a genome, in DNA alphabet e.g. tRNA, rRNA

See also[edit]

References[edit]

  1. ^ Tao Tao (2011-08-24). "Single Letter Codes for Nucleotides". NCBI Learning Center. National Center for Biotechnology Information. Retrieved 2012-03-15. 
  2. ^ "IUPAC code table". NIAS DNA Bank. 

External links[edit]