[BiO BB] Restriction sites frequencies in mouse genome

Martin Gollery marty.gollery at gmail.com
Mon Aug 28 09:30:42 EDT 2006

You are correct, BLAST is limited in the number of HSP extensions, and so
will not be appropriate for this type of search. I could run it for you with
TeraBlast, which has no such restrictions, but I think restrict from EMBOSS
will be the best tool for this.


On 8/28/06, Benoit VARVENNE <varvenne at genoway.com> wrote:
> Dear Members,
> I am a new member of this mailing-list and i don't know if such a post
> will
> draw the attention of anyone here. So excuse me in advance if my subject
> is
> not appropriate.
> I am searching for a way to calculate restriction sites frequency in mouse
> genome (so sequences from 6 to 13bp). I have already tried to do so using
> blast (or blast-like) tools and configuring them as needed but it gave no
> results, because of too numerous hits i think.
> I would be very greatful if someone could help me on this topic.
> Thanks a lot for your help,
> Best regards,
> Benoît Varvenne,
> Bioinformatics pearson in charge,
> Genoway Lyon - France
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Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
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