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.
<br><br>Marty<br><br><div><span class="gmail_quote">On 8/28/06, <b class="gmail_sendername">Benoit VARVENNE</b> <<a href="mailto:email@example.com">firstname.lastname@example.org</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Members,<br><br>I am a new member of this mailing-list and i don't know if such a post will<br>draw the attention of anyone here. So excuse me in advance if my subject is<br>not appropriate.<br>I am searching for a way to calculate restriction sites frequency in mouse
<br>genome (so sequences from 6 to 13bp). I have already tried to do so using<br>blast (or blast-like) tools and configuring them as needed but it gave no<br>results, because of too numerous hits i think.<br><br>I would be very greatful if someone could help me on this topic.
<br><br>Thanks a lot for your help,<br>Best regards,<br><br>Benoît Varvenne,<br>Bioinformatics pearson in charge,<br>Genoway Lyon - France<br><br>_______________________________________________<br>General Forum at Bioinformatics.Org
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>-- <br>Martin Gollery<br>Associate Director<br>Center For Bioinformatics<br>University of Nevada at Reno<br>Dept. of Biochemistry / MS330<br>775-784-7042<br>-----------