[BioC] Sequence alignment for DNA sequences

[A.J. Rossini]

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 at 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 at salk.edu
> >(Phone): 858-453-4100 ext 1105
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor at 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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> 


-- 
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 at gmail.com