[BioC] Sequence alignment for DNA sequences

[John Zhang]

>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
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084