[BioC] how to get mismatch or gap from pairwiseAlignment

[Martin Morgan]

On 04/27/2012 03:08 AM, Hervé Pagès wrote:
> 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

Here's how you find vignettes for the version of Biostrings installed on 
your computer

 > vignette(package="Biostrings") ## available vignettes
 > vignette(package="Biostrings", "PairwiseAlignments") ## a vignette

Martin

> 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
>>
>
>


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