[BioC] obtaining a complete global alignment via pairwiseAlignment

[Martin Morgan]

On 06/14/2013 07:57 PM, Robert K.Bradley [guest] wrote:
>
> Hello,
>
> I'm interested in using the pairwiseAlignment function in Biostrings to perform simple alignments of short sequences.  I noticed that even the global alignment mode returns an alignment with gapped ends trimmed off.  For example:
>
>> s1 = DNAString ("AAGGAA")
>> s2 = DNAString ("GG")
>> pairwiseAlignment (s1, s2, type = "global")
> Global PairwiseAlignmentsSingleSubject (1 of 1)
> pattern: [3] GG
> subject: [1] GG
> score: -32.03649
>
> Is it possible to obtain the complete alignment including the (possibly) gapped ends?  In this case, that would be:
> --GG--
> AAGGAA
> For my purposes, having the complete gapped alignment is important.

Hi Robert -- Not an expert on pairwiseAlignment, but I think the return value is 
a class that contains more information than it is showing

     > xx = pairwiseAlignment(s2, s1, type="global")
     > class(xx)
     [1] "PairwiseAlignmentsSingleSubject"
     attr(,"package")
     [1] "Biostrings"
     > class?PairwiseAlignmentsSingleSubject
     > aligned(xx)
       A DNAStringSet instance of length 1
         width seq
     [1]     6 --GG--

Martin

>
> My question seems related to a previous post:
> https://stat.ethz.ch/pipermail/bioconductor/2012-February/043577.html
>
> Thank you in advance.
>
> Best wishes,
> Rob
>


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