Sequence alignment: Difference between revisions

Revision as of 05:56, 22 November 2021

Revision as of 00:42, 6 January 2022

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===CIGAR Format===

Ref. : GTCGTAGAATA <br />

[[Read (biology)|Read]]: CACGTAG—TA <br />

CIGAR: 2S5M2D2M

where: <br />

2S = 2 soft clipping (could be mismatches, or a read longer than the matched sequence) <br />

5M = 5 matches or mismatches <br />

2D = 2 deletions <br />

2M = 2 matches or mismatches<br/>

The original CIGAR format from the [https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate alignment program] did not distinguish between mismatches or matches with the M character.

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| X||8||sequence mismatch||yes||yes

|-

|

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* “Consumes query” and “consumes reference” indicate whether the CIGAR operation causes the alignment to step along the query sequence and the reference sequence respectively.

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* [[UGENE]]

* [[Needleman–Wunsch algorithm]]

* [[Smith–Waterman algorithm|Smith-Waterman alogrithm]]

==References==

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{{Wikiversity|Dot-matrix methods}}

{{Spoken Wikipedia|En-Sequence_alignment.ogg|date=2012-06-05}}

* {{Commons category-inline}}

{{Bioinformatics}}