Hi Alessia,
you may want to post this kind of question on Bioc mailing list, 
is more appropriate.


 http://www.bioconductor.org/docs/mailList.html
About your question ,
I'm not 100% sure, but check  if Biostrings  pkg
can do what you need to do.

http://www.bioconductor.org/workshops/2008/SeattleNov08/MatchAlign/

Best Regards

Anna


Anna Freni Sterrantino
Ph.D Student 
Department of Statistics
University of Bologna, Italy
via Belle Arti 41, 40124 BO.




________________________________
Da: Alessia Deglincerti <ald2010@med.cornell.edu>
A: r-help@r-project.org
Inviato: Martedì 9 dicembre 2008, 16:03:55
Oggetto: [R] motif search

Hi,

I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs..  I would like to look for enrichment of certain motifs in genomic sequences.

I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs..

Thanks

A

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