[Bioperl-l] amino acid index
Heikki Lehvaslaiho
heikki@ebi.ac.uk
Thu, 04 Jul 2002 13:37:39 +0100
Navdeep,
How about Bio::ProteinProperty::AAIndex?
First you better think how to represent the index information. You need a
class for that, You could put that in
Bio::Tools::AAIndex::Index or Bio::ProteinProperty::AAindex::Index.
Bio::ProteinProperty::AAIndex::Indexer could know about a Index and a
protein sequence (Bio::PrimarySeqI object with alphabet('protein')).
Then you need to think how to get a index.
Bio::ProteinProperty::AAIndex::IO.pm could read and write the flat file
format with the help of Bio::ProteinProperty::AAIndex::IO::aaindex.pm
module, - or if you think there ever will be only flat fie format the Index
class could do the IO.
Next you need to get the indexes. If it comes over the web from the AAIndex
database, write a module Bio::DB::AAIndex. There are many other options
if plan to support local databases.
-Heikki
Navdeep Jaitly wrote:
> I was planning to write some for my use, if there wasn't an
> implementation already. I could make it available / submit changes to
> the bioperl cvs.
> I think Bio::Tools::AAIndex would be a good place to provide AAIndex
> access. Comments/suggestions ?
> Deep
>
>
>
>> From: Heikki Lehvaslaiho <heikki@ebi.ac.uk>
>> To: Navdeep Jaitly <ndjaitly@hotmail.com>
>> CC: bioperl-l@bioperl.org
>> Subject: Re: [Bioperl-l] amino acid index
>> Date: Thu, 04 Jul 2002 09:16:12 +0100
>> MIME-Version: 1.0
>> Received: from mc1-f28.law16.hotmail.com ([65.54.236.35]) by
>> mc1-s14.law16.hotmail.com with Microsoft SMTPSVC(5.0.2195.4905); Thu,
>> 4 Jul 2002 01:32:50 -0700
>> Received: from pw600a.bioperl.org ([199.93.107.70]) by
>> mc1-f28.law16.hotmail.com with Microsoft SMTPSVC(5.0.2195.4905); Thu,
>> 4 Jul 2002 01:32:28 -0700
>> Received: from pw600a.bioperl.org (localhost [127.0.0.1])by
>> pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g647AsGV024555;Thu, 4
>> Jul 2002 03:10:54 -0400
>> Received: from alpha1.ebi.ac.uk (alpha1.ebi.ac.uk [193.62.196.122])by
>> pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g6479FGV024538for
>> <bioperl-l@bioperl.org>; Thu, 4 Jul 2002 03:09:16 -0400
>> Received: from ebi.ac.uk (cetus.ebi.ac.uk [193.62.199.73])by
>> alpha1.ebi.ac.uk (8.9.3/8.9.3) with ESMTP id JAA322788;Thu, 4 Jul 2002
>> 09:16:12 +0100 (BST)
>> Message-ID: <3D24044C.7010303@ebi.ac.uk>
>> Organization: EMBL - EBI
>> User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP28; en-US; rv:0.9.9)
>> Gecko/20020313
>> X-Accept-Language: en-us, en
>> References: <F62nXOgf0tJ3nezS74800006b2e@hotmail.com>
>> Sender: bioperl-l-admin@bioperl.org
>> Errors-To: bioperl-l-admin@bioperl.org
>> X-BeenThere: bioperl-l@bioperl.org
>> X-Mailman-Version: 2.0.6
>> Precedence: bulk
>> List-Help: <mailto:bioperl-l-request@bioperl.org?subject=help>
>> List-Post: <mailto:bioperl-l@bioperl.org>
>> List-Subscribe:
>> <http://bioperl.org/mailman/listinfo/bioperl-l>,<mailto:bioperl-l-request@bioperl.org?subject=subscribe>
>>
>> List-Id: Bioperl Project Discussion List <bioperl-l.bioperl.org>
>> List-Unsubscribe:
>> <http://bioperl.org/mailman/listinfo/bioperl-l>,<mailto:bioperl-l-request@bioperl.org?subject=unsubscribe>
>>
>> List-Archive: <http://bioperl.org/pipermail/bioperl-l/>
>> Return-Path: bioperl-l-admin@bioperl.org
>> X-OriginalArrivalTime: 04 Jul 2002 08:32:28.0444 (UTC)
>> FILETIME=[54E6B5C0:01C22335]
>>
>>
>> There isn't. Are planning to write something?
>>
>> -Heikki
>>
>>
>>
>> Navdeep Jaitly wrote:
>>
>>> Hi!
>>> Is there any on-going work that would allow users to calculate
>>> AAIndex values for a peptide by specifying an accession number for an
>>> AAIndex ?
>>> Cheers!
>>> Deep
>>>
>>>
>>> _________________________________________________________________
>>> Chat with friends online, try MSN Messenger: http://messenger.msn.com
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@bioperl.org
>>> http://bioperl.org/mailman/listinfo/bioperl-l
>>
>>
>>
>> --
>> ______ _/ _/_____________________________________________________
>> _/ _/ http://www.ebi.ac.uk/mutations/
>> _/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk
>> _/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
>> _/ _/ _/ Wellcome Trust Genome Campus, Hinxton
>> _/ _/ _/ Cambs. CB10 1SD, United Kingdom
>> _/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
>> ___ _/_/_/_/_/________________________________________________________
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-l
>
>
>
>
>
> _________________________________________________________________
> Join the world?s largest e-mail service with MSN Hotmail.
> http://www.hotmail.com
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
--
______ _/ _/_____________________________________________________
_/ _/ http://www.ebi.ac.uk/mutations/
_/ _/ _/ Heikki Lehvaslaiho heikki@ebi.ac.uk
_/_/_/_/_/ EMBL Outstation, European Bioinformatics Institute
_/ _/ _/ Wellcome Trust Genome Campus, Hinxton
_/ _/ _/ Cambs. CB10 1SD, United Kingdom
_/ Phone: +44 (0)1223 494 644 FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________