[BioC] obtaining a complete global alignment via pairwiseAlignment

[Robert K. Bradley]

Thanks Martin.  as.character (aligned (...)) does return a gapped string 
for one of the two aligned sequences, but even that command trims off 
unaligned characters.  For example:
For example:
 > s1 = DNAString ("AGGGG")
 > s2 = DNAString ("GGGGA")
 > xx = pairwiseAlignment (s1, s2, gapOpening = -1)
 > as.character (xx)
[1] "GGGG-"
while the whole gapped string is "AGGGG-".

I apologize in advance if I'm missing something obvious here.

Best,
Rob

On 6/15/13 6:45 AM, Martin Morgan wrote:
> 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
>>
>
>