FASTA format - Revision history

Christoph: /* See also */

2012-07-13T23:02:49Z

‎See also

Christoph at 03:02, 5 August 2007

2007-08-05T03:02:08Z

Christoph at 08:37, 29 December 2006

2006-12-29T08:37:13Z

Christoph: Started article

2006-01-23T22:49:30Z

Started article

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In [[:Category:Bioinformatics|bioinformatics]], '''FASTA format''' is a file format used to exchange information between genetic sequence databases.

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. An example FASTA format:

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

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). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown nucleic acid residue or X for unknown amino acid residue).

The nucleic acid codes supported are:
{| style="border:solid 1px black;"
! Nucleic Acid Code
! Meaning
|-
| A
| [[adenosine|'''A'''denosine]]
|-
| C
| [[cytidine|'''C'''ytidine]]
|-
| G
| [[guanine|'''G'''uanine]]
|-
| T
| [[thymidine|'''T'''hymidine]]
|-
| U
| [[uracil|'''U'''racil]]
|-
| R
| G A ([[purine|pu'''R'''ine]])
|-
| Y
| T C ([[pyrimidine|p'''Y'''rimidine]])
|-
| K
| G T ([[ketone|'''K'''etone]])
|-
| M
| A C ([[amino|a'''M'''ino group]])
|-
| S
| G C ('''S'''trong interaction)
|-
| W
| A T ('''W'''eak interaction)
|-
| B
| G T C (not A) ('''B''' comes after A)
|-
| D
| G A T (not C) ('''D''' comes after C)
|-
| H
| A C T (not G) ('''H''' comes after G)
|-
| V
| G C A (not T, not U) ('''V''' comes after U)
|-
| N
| A G C T (a'''N'''y)
|-
| -
| gap of indeterminate length
|}

The amino acid codes supported are:
{| style="border:solid 1px black;"
! Amino Acid Code
! Meaning
|-
| A
| [[Alanine]]
|-
| B
| [[Aspartic_acid|Aspartic acid]] or [[Asparagine]]
|-
| C
| [[Cysteine]]
|-
| D
| [[Aspartate]]
|-
| E
| [[Glutamate]]
|-
| F
| [[Phenylalanine]]
|-
| G
| [[Glycine]]
|-
| H
| [[Histidine]]
|-
| I
| [[Isoleucine]]
|-
| K
| [[Lysine]]
|-
| L
| [[Leucine]]
|-
| M
| [[Methionine]]
|-
| N
| [[Asparagine]]
|-
| P
| [[Proline]]
|-
| Q
| [[Glutamine]]
|-
| R
| [[Arginine]]
|-
| S
| [[Serine]]
|-
| T
| [[Threonine]]
|-
| U
| [[Selenocysteine]]
|-
| V
| [[Valine]]
|-
| W
| [[Tryptophan]]
|-
| Y
| [[Tyrosine]]
|-
| Z
| [[Glutamate]] or [[Glutamine]]
|-
| X
| any
|-
| *
| translation stop
|-
| -
| gap of indeterminate length
|}

== Syntax ==
A FASTA format looks like the following:

<pre>
>SEQUENCE_1
;comment line 1 (optional)
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
;comment line 1 (optional)
;comment line 2 (optional)
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
</pre>

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 sequence. 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]). This should be interpreted as both headers pointing to the same sequence below.

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: each line of a sequence should have fewer than 80 characters. Sequences may be protein sequences or DNA sequences, and they can contain gaps or alignment characters (see sequence alignment).

FASTA format files often have file extensions like .fa, .fasta, or .fsa.

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 definitive 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

The vertical bars in the above list are not separators in the sense of the Backus-Naur form, but are part of the format.

== External links ==
* [http://en.wikipedia.org/wiki/FASTA_format Wikipedia article on '''FASTA format''']
* [http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in Sequence Formats]
* [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI's FASTA format description]
* [http://www.binf.ku.dk/~kasper/misc/lfasta/ LFasta]
* [http://www.cyber-indian.com/bioperl/index.html mGen] — containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction

[[Category:Academic Research]]
[[Category:Bioinformatics]]

@@ Line 202: / Line 202: @@
 ==See also==
 *[[LFasta]]
-*[[BLAST]]
+*[[BLAST]] / [[BLAST+]]
 *[[Blastall]]
 *[[Formatdb]]
 ==External links==

@@ Line 201: / Line 201: @@
 ==See also==
-* [[BLAST]]
+*[[LFasta]]
-* [[Blastall]]
+*[[BLAST]]
-* [[Formatdb]]
+*[[Blastall]]
-== External links ==
+==External links==
-* [http://en.wikipedia.org/wiki/FASTA_format Wikipedia article on '''FASTA format''']
+*[http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in Sequence Formats]
-* [http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#in Sequence Formats]
+*[http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI's FASTA format description]
-* [http://www.ncbi.nlm.nih.gov/blast/fasta.shtml NCBI's FASTA format description]
+*[http://www.binf.ku.dk/~kasper/misc/lfasta/ LFasta]
-* [http://www.binf.ku.dk/~kasper/misc/lfasta/ LFasta]
+*[http://www.cyber-indian.com/bioperl/index.html mGen] &mdash; containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
-* [http://www.cyber-indian.com/bioperl/index.html mGen] &mdash; containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
+*[[wikipedia:FASTA_format]]
 [[Category:Bioinformatics]]

@@ Line 170: / Line 170: @@
 </pre>
-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 sequence. 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]). This should be interpreted as both headers pointing to the same sequence below.
+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 standardized headers, which helps when automatically extracting information from the header. Often the first 'word' of the header is a unique identifier for the sequence. 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]). This should be interpreted as both headers pointing to the same sequence below.
 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.
@@ Line 199: / Line 199: @@
 The vertical bars in the above list are not separators in the sense of the Backus-Naur form, but are part of the format.
 == External links ==
@@ Line 207: / Line 212: @@
 * [http://www.cyber-indian.com/bioperl/index.html mGen] &mdash; containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
 [[Category:Bioinformatics]]