[BioC] feature request - pairwiseAlignment() in Biostrings

Patrick Aboyoun paboyoun at fhcrc.org
Thu Jul 22 19:26:48 CEST 2010


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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