Sequence alignment for DNA sequences
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Fangxin Hong ▴ 810
@fangxin-hong-912
Last seen 7.9 years ago
Hi list, I am wondering whether there is a package which can do sequence alignment for DNA sequences. I know package pairseqsim, which is applied to amino acid sequence. And I believe it is fairly simple to change it so that it will apply to nucleotide sequence, have anybody done that? Can I ask for some code? Thank you very much. Fangxin -------------------- Fangxin Hong Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu (Phone): 858-453-4100 ext 1105
pairseqsim pairseqsim • 775 views
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 7.9 years ago
>I am wondering whether there is a package which can do sequence alignment >for DNA sequences. I know package pairseqsim, which is applied to amino >acid sequence. And I believe it is fairly simple to change it so that it >will apply to nucleotide sequence, have anybody done that? Can I ask for >some code? Have a look at the Biostrings package. > >Thank you very much. >Fangxin > > > >-------------------- >Fangxin Hong Ph.D. >Plant Biology Laboratory >The Salk Institute >10010 N. Torrey Pines Rd. >La Jolla, CA 92037 >E-mail: fhong@salk.edu >(Phone): 858-453-4100 ext 1105 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
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I was thinking that ape (in CRAN) did automatic alignment, but I was wrong. There is a BioSeq1 package which does have an interface to clustal which might be useful; it really needs to incorporate the BioStrings data structures to be really useful, though. I can send it if it is of interest. (it may or may not work; and would be a source package, not a binary package, requiring some building -- it used to work). best, -tony On 5/17/05, John Zhang <jzhang@jimmy.harvard.edu> wrote: > > >I am wondering whether there is a package which can do sequence alignment > >for DNA sequences. I know package pairseqsim, which is applied to amino > >acid sequence. And I believe it is fairly simple to change it so that it > >will apply to nucleotide sequence, have anybody done that? Can I ask for > >some code? > > Have a look at the Biostrings package. > > > > > >Thank you very much. > >Fangxin > > > > > > > >-------------------- > >Fangxin Hong Ph.D. > >Plant Biology Laboratory > >The Salk Institute > >10010 N. Torrey Pines Rd. > >La Jolla, CA 92037 > >E-mail: fhong@salk.edu > >(Phone): 858-453-4100 ext 1105 > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- best, -tony "Commit early,commit often, and commit in a repository from which we can easily roll-back your mistakes" (AJR, 4Jan05). A.J. Rossini blindglobe@gmail.com
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