[BiO BB] Restriction sites frequencies in mouse genome

[Benoit VARVENNE]

Hello Gary,

Thanks a lot for your suggestions.
I've got Perl programming capabilities and i'm already used to Bioperl
package but the aim is to perform operations using already existing
softwares which allow me calculate frequencies (so number of hits...)
without any additive programming and using web tools (software+genome).
The problem encountered is that all softwares i've already found (including
LaserGene i think) seem to be useful for finding restriction sites in
sequences given in parameter (so not in a whole genome).

If i found such a solution i'm going to post it here if someone's
interested.

Thanks again for your very quick answer,
Best regards,

Benoît Varvenne
Bioinformatics pearson in charge,
Genoway Lyon - France

Le 28/08/06 14:37, « Gary Van Domselaar » <gary at primary.bioinformatics.org>
a écrit :

> 
> Hi Beno,
> 
> If you Perl programming capability, you should use the bioperl libraries:
> http://bioperl.org
> http://www.bioperl.org/wiki/Bptutorial.pl
> http://www.bioperl.org/wiki/Bptutorial.pl#III.3.4_Identifying_restriction_enzy
> me_sites_.28Bio::Restriction.29
> 
> You may also be able to calculate restriction site frequencies with
> bioinformatics software programs like LaserGene plus Excel.
> 
> Regards,
> 
> g.
> --
> Gary Van Domselaar, PhD
> Head of Bioinformatics
> National Microbiology Laboratory
> Public Health Agency of Canada
> 1015 Arlington St., Winnipeg, MB, Canada R3E 3R2
> 
> Suite H3570
> Ph: (204)-784-5994    Fax: (204)-789-2018
> gary_van_domselaar at phac-aspc.gc.ca
> gary.vandomselaar at gmail.com
> 
> 
> Associate Director, Bioinformatics.Org
> gary at bioinformatics.org
> 
> 
> 
> 
> On Mon, 28 Aug 2006, Benoit VARVENNE 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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