[BioC] how to get mismatch or gap from pairwiseAlignment

[Hervé Pagès]

Hi,

On 04/26/2012 06:18 PM, wang peter wrote:
> dear all:
> pairwiseAlignment {Biostrings} can only output aligment result
> if i need the number of mismatch or gap
> how can i extract those information?

The Biostrings package has an entire vignette dedicated to
pairwiseAlignment() and related tools. How to extract this kind
of information is explained in details. For example:

 > globalAlign
Global PairwiseAlignedFixedSubject (1 of 1)
pattern: [1] ACTTCACCAGCTCCCTGGCGGTAAGTTGATC---AAAGG---AAACGCAAAGTTTTCAAG
subject: [1] GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC
score: -52

 > nmatch(globalAlign)
[1] 33

 > nmismatch(globalAlign)
[1] 21

 > nindel(pattern(globalAlign))
      Length WidthSum
[1,]      2        6

Cheers,
H.

>
> thank you
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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