That's perfect.  Thanks for the quick response.

Andrew

On Wed, Apr 28, 2010 at 8:16 PM, Patrick Aboyoun <paboyoun@fhcrc.org> wrote:

> Andrew,
>
> start(subject(myalign))
>
> should get you what you are looking for.
>
> Cheers,
> Patrick
>
>
>
> On 4/28/10 5:07 PM, Andrew Yee wrote:
>
>> I'm using pairwiseAlignment() in the Biostrings package as follows:
>>
>>
>> library('Biostrings')
>>
>> pattern<- DNAString('GCGAGAG')
>> subject<- DNAString('AGCTTTAGAGGCGAGAGGCAT')
>>
>> myalign<- pairwiseAlignment(pattern, subject)
>> subject(myalign)
>>
>>
>>
>>> subject(myalign)
>>>
>>>
>> [11] GCGAGAG
>>
>> I'm interested in the position where the pattern starts aligning with the
>> subject.  In this case, subject(myalign) gives 11 as the starting position
>> as part of the print out.  Is there a way to pull out this starting
>> position
>> information from subject(myalign)?
>>
>> Thanks,
>> Andrew
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>
>

	[[alternative HTML version deleted]]

