[BioC] DNA sequence analysis question

[Steve Lianoglou]

Hi,

On Wed, Mar 14, 2012 at 11:25 AM, andigoni <andigoni at gmail.com> wrote:
>
> Is there any package for motif finding in DNA sequences that uses consensus
> matrices as input?

Does the `matchPWM` function in the Biostrings package do what you're
looking for?

> In addition, I need to extract genomic features e.g. exons, intron, utr,
> splice sites etc. given the genomic coordinates for multiple sequences. Is
> there any package for such analyses?

Can you explain this a bit more? Do you want to, say, use a GRanges
object to query what "type" of genomic annotation is there (intron,
cds, utr, etc)?

If that's the case, at the previous bioc workshop in Feb, it seemed
like several people hacked up their own way to do things like that.

I believe Valerie has put something "more official" together somewhere
in her "VariantAnnotation" package that you might like to use.

See section 3 (Variant location) in the VriantAnnotation pdf:
http://www.bioconductor.org/packages/devel/bioc/vignettes/VariantAnnotation/inst/doc/VariantAnnotation.pdf

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact