Toughest question is probably not how to modify the C code, but how the
results will be represented and manipulated in R.

Good luck

On Thu, Jul 22, 2010 at 10:26 AM, Patrick Aboyoun <paboyoun@fhcrc.org>wrote:

> Avril,
> I wont have time to extend pairwiseAlignment, but you are more then welcome
> to. It is written mainly in C with an R wrapper. You can grab it via svn at
> the URL
>
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings
>
> with username: readonly and password: readonly.
>
> The particular files you'll want to look at are
>
>
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings/src/align_pairwiseAlignment.c
>
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrings/R/pairwiseAlignment.R
>
> I can provide you with a code walkthrough if you like. Since I optimized
> the code for speed and memory usage, you may find it is easier to write your
> own C level function that will be used instead of the code I have since I
> don't keep enough information around to be able to select the top X
> alignments.
>
>
> Cheers,
>
> Patrick
>
>
>
> On 7/22/10 1:54 AM, Coghlan, Avril wrote:
>
>> Dear Patrick and Steve,
>>
>> I am wondering whether it would be possible to add an option to the
>> pairwiseAlignment() function in Biostrings, so that it could print out:
>> (i) all the top-scoring alignments for 2 sequences, if there are more
>> than one equally scoring top-scoring alignments ?
>> (ii) the top X top-scoring alignments for 2 sequences, where the user
>> specifies the number X, and where the X alignments don't have to have
>> equal scores, but are ordered by decreasing score ?
>>
>> I'm not sure if these options are easy to add, but would be very useful
>> if you could add them.
>>
>> If you haven't time to do this, I would be willing to try to help add
>> the features to the pairwiseAlignment() function, if you can point me
>> towards the code.
>>
>> Kind Regards,
>> Avril
>>
>> Avril Coghlan
>> University College Cork
>> Ireland
>>
>>
>>
>>
>>
>>
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