[Bioperl-l] Finding seqs of given domain architecture

Jacob Keller j-keller2 at md.northwestern.edu
Wed Apr 16 12:12:27 EDT 2008


Hello All,

I am new to this list, so am not totally sure this is the right forum, so 
please forgive if this is not the right place to asl the following question: 
I am seeking to get all sequences that have a given domain architecture, or 
at least that contain two given domains. I have thought of a few ways to do 
this.

1. Blast/Psi-blast for each domain, then compare the results for common 
sequences between the two lists, and fetch those. I would need to write a 
(simple) script to do this, but would prefer not to re-invent the wheel.

2. Search with a paradigm sequence of desired architecture/domain 
composition, somehow tweaking the psiblast parameters to find only matches 
over the whole search sequence, thereby finding both desired domains. I am 
not sure how to tweak blast to do this, though.

3. Pfam has this capability, i.e. to show all domains with a given 
architecture, but it is difficult to get at the actual sequences or even a 
list of accession numbers.

Does anybody have any suggestions as to how optimally to get these seq's?

Thanks for your consideration,

Jacob

*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-keller2 at northwestern.edu
*******************************************

----- Original Message ----- 
From: "Heikki Lehvaslaiho" <heikki at sanbi.ac.za>
To: <bioperl-l at lists.open-bio.org>
Cc: <allenday at ucla.edu>; "Chris Fields" <cjfields at uiuc.edu>; "Jay Hannah" 
<jay at jays.net>; <bioperl-l at bioperl.org>
Sent: Wednesday, April 16, 2008 6:36 AM
Subject: Re: [Bioperl-l] bioperl-microarray: status?


> FYI,
>
> Christoper Jones has just published
> [http://bioinformatics.oxfordjournals.org/cgi/content/short/24/8/1102 an
> article in Bioinformatics] about his
> [http://search.cpan.org/perldoc?Microarray Microarray perl module] in 
> CPAN.
>
> (The text added into BioPerl wiki.)
>
> -Heikki
>
>
> On Friday 26 January 2007 16:05:01 Chris Fields wrote:
>> Don't know if it's worth it, but could the microarray package be
>> modified so that it deals with data generated from or interacts
>> directly with Bioconductor (i.e. maybe including some specialized
>> bioperl-run set of classes to run Bioconductor tasks, return
>> lightweight bioperl microarray classes)?  Allen pointed out in a
>> previous post that Bioconductor is the best pick for certain tasks,
>> while Perl excels at others:
>>
>> http://article.gmane.org/gmane.comp.lang.perl.bio.general/13993
>>
>> Might be nice if we could merge both strengths together in some way.
>>
>> chris
>>
>> On Jan 26, 2007, at 7:26 AM, Jay Hannah wrote:
>> > On Jan 25, 2007, at 2:30 AM, Allen Day wrote:
>> >> Eh, there is some discussion activity on the list, but not much.  You
>> >> are really better off moving to Bioconductor.
>> >
>> > Ok, thanks. I added that to the wiki page:
>> >
>> >     http://www.bioperl.org/wiki/Microarray_package
>> >
>> > j
>> > seqlab.net
>> > http://www.bioperl.org/wiki/User:Jhannah
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> -- 
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>      _/      _/
>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>  _/  _/  _/  University of Western Cape, South Africa
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