[BiO BB] finding repeat sequences

[Matthias Gallé]

Let me also recommend vmatch (http://www.vmatch.de/), that search for
maximal repeats. It is not open source nor can it be downloaded
immediately, but a free of charge licence can be obtained by sending
an email to its developer (Stefan Kurtz)

On Tue, Dec 9, 2008 at 18:38, Seema Trivedi <svtrived at hotmail.com> wrote:
>
> Hi
> One program is SPUTNIK at the following link http://espressosoftware.com/pages/sputnik.jsp
> but one will have to modify it a bit to take longer sequences as it analyzes only short seq. You can also use the online version of the same at http://cbi.labri.fr/outils/Pise/sputnik.html.
> The modified version of this program is available possibly with MORGANTE
>            MICHELE michele.morgante at dpvta.uniud.it as indicated in the following link http://bioinf.dimi.uniud.it/software/software/sputnik. However, do not know the drawbacks of this modified version.
>
> Seema Trivedi
>
>
>
>
>> Date: Mon, 8 Dec 2008 09:55:11 -0800
>> From: idoerg at gmail.com
>> To: bbb at bioinformatics.org
>> Subject: Re: [BiO BB] finding repeat sequences
>>
>> http://tandem.bu.edu/trf/trf.html
>>
>>
>>
>> On Fri, Dec 5, 2008 at 9:05 PM, jalil fallah <jalil.fallah at gmail.com> wrote:
>>
>> > Dear all ,
>> >
>> > I was wondering if you would mind answering my request.
>> > How could I access to a software or a database to find tandem repeat
>> > sequences in a prokaryotic gene ?
>> >
>> > Thank you in advance
>> >
>> >
>> > --
>> > Jalil Fallah
>> > Ph.D Candidate of Medical Bacteriology
>> > Dep. of Bacteriology
>> > School of Medicine
>> > Tarbiat Modarres University
>> > Tehran - Iran
>> > P.O.Box 14115-331
>> > Cell Phone +98- 912- 5093060
>> > _______________________________________________
>> > BBB mailing list
>> > BBB at bioinformatics.org
>> > http://www.bioinformatics.org/mailman/listinfo/bbb
>> >
>>
>>
>>
>> --
>> Iddo Friedberg, Ph.D.
>> Atkinson Hall, mail code 0446
>> University of California, San Diego
>> 9500 Gilman Drive
>> La Jolla, CA 92093-0446, USA
>> T: +1 (858) 534-0570
>> http://iddo-friedberg.org
>> _______________________________________________
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>
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-- 
Matthias Gallé

Gaudeamus igitur