Editing FASTA format (section)

==Description line==

The description line (defline) or header/identifier 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 [[William Pearson (scientist)|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 [https://www.ncbi.nlm.nih.gov/blast/fasta.shtml the NCBI FASTA specification]. An example of a multiple sequence FASTA file follows:

<syntaxhighlight lang="text">
>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
</syntaxhighlight>

=== NCBI identifiers ===
The [[National Center for Biotechnology Information|NCBI]] defined a standard for the unique identifier used for the sequence (SeqID) in the header line.  This allows a sequence that was obtained from a database to be labelled with a reference to its database record.  The database identifier format is understood by the NCBI tools like <code>makeblastdb</code> and <code>table2asn</code>. The following list describes the NCBI FASTA defined format for sequence identifiers.<ref>{{cite book |title=NCBI C++ Toolkit Book |publisher=National Center for Biotechnology Information |url=https://ncbi.github.io/cxx-toolkit/pages/ch_demo#ch_demo.id1_fetch.html_ref_fasta |access-date=2018-12-19}}</ref>

{| class="wikitable sortable" style="border: 1px solid black; margin-bottom: 10px;"
|-
! Type
! Format(s)
! Example(s)
|-
| local (i.e. no database reference)
| <code>lcl&#124;''integer''</code><br />
<code>lcl&#124;''string''</code>
| <code>lcl&#124;123</code><br />
<code>lcl&#124;hmm271</code>
|-
| GenInfo backbone seqid
| <code>bbs&#124;''integer''</code>
| <code>bbs&#124;123</code>
|-
| GenInfo backbone moltype
| <code>bbm&#124;''integer''</code>
| <code>bbm&#124;123</code>
|-
| GenInfo import ID
| <code>gim&#124;''integer''</code>
| <code>gim&#124;123</code>
|-
| [https://www.ncbi.nlm.nih.gov/Genbank/index.html GenBank]
| <code>gb&#124;''accession''&#124;''locus''</code>
| <code>gb&#124;M73307&#124;AGMA13GT</code>
|-
| [http://www.embl-heidelberg.de EMBL]
| <code>emb&#124;''accession''&#124;''locus''</code>
| <code>emb&#124;CAM43271.1&#124;</code>
|-
| [https://web.archive.org/web/20140312021627/http://pir.georgetown.edu/ PIR]
| <code>pir&#124;''accession''&#124;''name''</code>
| <code>pir&#124;&#124;G36364</code>
|-
| [http://www.ebi.ac.uk/swissprot SWISS-PROT]
| <code>sp&#124;''accession''&#124;''name''</code>
| <code>sp&#124;P01013&#124;OVAX_CHICK</code>
|-
| patent
| <code>pat&#124;''country''&#124;''patent''&#124;''sequence-number''</code>
| <code>pat&#124;US&#124;RE33188&#124;1</code>
|-
| pre-grant patent
| <code>pgp&#124;''country''&#124;''application-number''&#124;''sequence-number''</code>
| <code>pgp&#124;EP&#124;0238993&#124;7</code>
|-
| [https://www.ncbi.nlm.nih.gov/projects/RefSeq RefSeq]
| <code>ref&#124;''accession''&#124;''name''</code>
| <code>ref&#124;NM_010450.1&#124;</code>
|-
| general database reference<br />(a reference to a database that's not in this list)
| <code>gnl&#124;''database''&#124;''integer''</code><br />
<code>gnl&#124;''database''&#124;''string''</code>
| <code>gnl&#124;taxon&#124;9606</code><br />
<code>gnl&#124;PID&#124;e1632</code>
|-
| GenInfo integrated database
| <code>gi&#124;''integer''</code>
| <code>gi&#124;21434723</code>
|-
| [http://www.ddbj.nig.ac.jp DDBJ]
| <code>dbj&#124;''accession''&#124;''locus''</code>
| <code>dbj&#124;BAC85684.1&#124;</code>
|-
| [http://www.prf.or.jp PRF]
| <code>prf&#124;''accession''&#124;''name''</code>
| <code>prf&#124;&#124;0806162C</code>
|-
| [https://web.archive.org/web/20080828002005/http://www.rcsb.org./pdb PDB]
| <code>pdb&#124;''entry''&#124;''chain''</code>
| <code>pdb&#124;1I4L&#124;D</code>
|-
| third-party [https://www.ncbi.nlm.nih.gov/Genbank/index.html GenBank]
| <code>tpg&#124;''accession''&#124;''name''</code>
| <code>tpg&#124;BK003456&#124;</code>
|-
| third-party [http://www.embl-heidelberg.de EMBL]
| <code>tpe&#124;''accession''&#124;''name''</code>
| <code>tpe&#124;BN000123&#124;</code>
|-
| third-party [http://www.ddbj.nig.ac.jp DDBJ]
| <code>tpd&#124;''accession''&#124;''name''</code>
| <code>tpd&#124;FAA00017&#124;</code>
|-
| TrEMBL
| <code>tr&#124;''accession''&#124;''name''</code>
| <code>tr&#124;Q90RT2&#124;Q90RT2_9HIV1</code>
|}

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, also separated by vertical bars.