[BiO BB] Consensus Sequence Plots

[Mike Marchywka]

I've written some scripts to parse and format clustalw output. For something
that large you may want native code but, alternatively, if these really
come from clustalw the source code is available so you
can do whatever you want. I would point out, however, that
you may need to be careful with specifics. I've tried getting clustal
to align individual probes to a gene and had better luck, for my
purposes, with simplistic no-gap code. Anytime you start using
tools in different regions of parameter space it may be important
to have ways to validate them. Scripts often work here as they
can be quick to write but slow to execute- just what you want
for validation but not production.

In short- try cygwin or even debian.





>From: "lijo skb" <lijo.skb at gmail.com>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>Subject: Re: [BiO BB] Consensus Sequence Plots
>Date: Thu, 7 Jun 2007 14:26:31 +0530
>
>Y can't you seek help from www.sooryakiran.com, kiran.soorya at gmail.com. 
>They
>are pretty good guys in assiting bioinformatcians.
>
>regards
>Li
>
>
>On 6/7/07, Sipos Botond <sbotond at gmail.com> wrote:
>>
>>Hello!
>>
>>I think sequence logos may be useful for this problem.
>>http://weblogo.berkeley.edu/
>>
>>Botond.
>>
>>
>>
>>On 6/6/07, Daniel Harari <lcharari at yahoo.com > wrote:
>> >
>> > Dear all,
>> >
>> > I am in need of a program that will have the capacity to scan large
>>files
>> > of multiple sequence protein alignments ( e.g 2500 sequences of a
>>protein
>> > 500 amino acids in length), in the search regions of consensus
>> > sequences.  The input alignment file will be in clustal or Muscle
>> > format.     I am looking for either a graphical or tabular
>>output,  where if
>> > possible, it would be able to home in on regions of interest and 
>>analyze
>> > them more thoroughly.
>> >
>> > Any recommendations would be very much appreciated.
>> >
>> > Regards,
>> >
>> > Daniel
>> >
>> >
>> > Daniel Harari, PhD.
>> > Chaim Orbach 15A.
>> > Rehovot, 76534
>> > ISRAEL
>> > Email:     daniel.harari at yahoo.com
>> > Phone:   +972-8-931-5943
>> > Mobile:   +972-544-241-168
>> >
>> > ---------------------------------
>> > Boardwalk for $500? In 2007? Ha!
>> > Play Monopoly Here and Now (it's updated for today's economy) at Yahoo!
>> > Games.
>> > _______________________________________________
>> > General Forum at Bioinformatics.Org -
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>> >
>>_______________________________________________
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>>
>
>
>
>--
>Lijo
>_______________________________________________
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

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