Editing FASTA format (section)

=={{anchor|Extended Format}}Extensions==
[[FASTQ format]] is a form of FASTA format extended to indicate information related to sequencing. It is created by the [[Sanger Centre]] in Cambridge.<ref name=fastq>{{cite journal | vauthors = Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM | title = The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants | journal = Nucleic Acids Research | volume = 38 | issue = 6 | pages = 1767–71 | date = April 2010 | pmid = 20015970 | pmc = 2847217 | doi = 10.1093/nar/gkp1137 }}</ref>

A2M/A3M are a family of FASTA-derived formats used for [[sequence alignment]]s. In A2M/A3M sequences, lowercase characters are taken to mean insertions, which are then indicated in the other sequences as the dot ("{{tt|.}}") character. The dots can be discarded for compactness without loss of information. As with typical FASTA files used in alignments, the gap ("{{tt|-}}") is taken to mean exactly one position.<ref>{{cite web |title=Description of A2M alignment format |url=https://compbio.soe.ucsc.edu/a2m-desc.html |url-status=dead |archive-url=https://web.archive.org/web/20220815104407/https://compbio.soe.ucsc.edu/a2m-desc.html |archive-date=2022-08-15 |work=[[SAMtools]]}}</ref> A3M is similar to A2M, with the added rule that gaps aligned to insertions can too be discarded.<ref>{{cite web |title=soedinglab/hh-suite: reformat.pl |url=https://github.com/soedinglab/hh-suite/blob/master/scripts/reformat.pl |website=GitHub |date=20 November 2022 |language=en}}</ref>