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/Biostrin gs/src/align_pairwiseAlignment.c > > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biostrin gs/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 >> >> >> >> >> >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]