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Question: feature request - pairwiseAlignment() in Biostrings
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gravatar for Coghlan, Avril
7.3 years ago by
Coghlan, Avril190 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
ADD COMMENTlink modified 7.3 years ago by Patrick Aboyoun1.6k • written 7.3 years ago by Coghlan, Avril190
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gravatar for Patrick Aboyoun
7.3 years ago by
Patrick Aboyoun1.6k
United States
Patrick Aboyoun1.6k 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 > > > > >
ADD COMMENTlink written 7.3 years ago by Patrick Aboyoun1.6k
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]]
ADD REPLYlink written 7.3 years ago by Michael Lawrence9.8k
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