[Bioclusters] [Fwd: [BiO BB] question on clustering]

Thu, 05 Aug 2004 19:21:40 -0400

This is a multi-part message in MIME format.
--------------060509080208070005030601
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Content-Transfer-Encoding: 7bit

--------------060509080208070005030601
Content-Type: message/rfc822;
 name="[BiO BB] question on clustering"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline;
 filename="[BiO BB] question on clustering"

Return-Path: <bio_bulletin_board-admin@bioinformatics.org>
Delivered-To: jeff@bioinformatics.org
Received: from localhost (localhost.localdomain [127.0.0.1])
	by www.bioinformatics.org (Postfix) with ESMTP
	id 6E5D4D1F3F; Thu,  5 Aug 2004 19:21:11 -0400 (EDT)
Received: from www.bioinformatics.org ([127.0.0.1])
 by localhost (www.bioinformatics.org [127.0.0.1:10024]) (amavisd-new)
 with ESMTP id 27699-10; Thu,  5 Aug 2004 19:21:06 -0400 (EDT)
Received: from www.bioinformatics.org (localhost.localdomain [127.0.0.1])
	by www.bioinformatics.org (Postfix) with ESMTP
	id C309FD1F1C; Thu,  5 Aug 2004 19:20:19 -0400 (EDT)
Delivered-To: bio_bulletin_board@bioinformatics.org
Received: from localhost (localhost.localdomain [127.0.0.1])
	by www.bioinformatics.org (Postfix) with ESMTP id 9367BD1F1C
	for <bio_bulletin_board@bioinformatics.org>; Thu,  5 Aug 2004 19:14:30 -0400 (EDT)
Received: from www.bioinformatics.org ([127.0.0.1])
 by localhost (www.bioinformatics.org [127.0.0.1:10024]) (amavisd-new)
 with ESMTP id 27699-05 for <bio_bulletin_board@bioinformatics.org>;
 Thu,  5 Aug 2004 19:14:29 -0400 (EDT)
Received: from grassmarket.ucs.ed.ac.uk (grassmarket.ucs.ed.ac.uk [129.215.166.64])
	by www.bioinformatics.org (Postfix) with ESMTP id 38D57D1F16
	for <bio_bulletin_board@bioinformatics.org>; Thu,  5 Aug 2004 19:14:27 -0400 (EDT)
Received: from grassmarket.ucs.ed.ac.uk (localhost [127.0.0.1])
	by grassmarket.ucs.ed.ac.uk (8.12.10/8.12.10) with ESMTP id i75NGmcn007644
	for <bio_bulletin_board@bioinformatics.org>; Fri, 6 Aug 2004 00:16:48 +0100 (BST)
Received: (from nobody@localhost)
	by grassmarket.ucs.ed.ac.uk (8.12.10/8.12.9/Submit) id i75NGlK7007640
	for bio_bulletin_board@bioinformatics.org; Fri, 6 Aug 2004 00:16:47 +0100 (BST)
From: FJPB Asselbergs <s0340567@sms.ed.ac.uk>
X-Authentication-Warning: grassmarket.ucs.ed.ac.uk: nobody set sender to s0340567@sms.ed.ac.uk using -f
Received: from 82-41-18-237.cable.ubr03.edin.blueyonder.co.uk (82-41-18-237.cable.ubr03.edin.blueyonder.co.uk [82.41.18.237]) 
	by sms.ed.ac.uk (IMP) with HTTP 
	for <s0340567@localhost>; Fri,  6 Aug 2004 00:16:47 +0100
Message-ID: <1091747807.4112bfdfb82f7@sms.ed.ac.uk>
To: bio_bulletin_board@bioinformatics.org
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-15
Content-Transfer-Encoding: 8bit
User-Agent: Internet Messaging Program (IMP) 3.2.3
X-Scanned-By: MIMEDefang 2.33 (www . roaringpenguin . com / mimedefang)
Subject: [BiO BB] question on clustering
Sender: bio_bulletin_board-admin@bioinformatics.org
Errors-To: bio_bulletin_board-admin@bioinformatics.org
X-BeenThere: bio_bulletin_board@bioinformatics.org
X-Mailman-Version: 2.0.8
Precedence: bulk
Reply-To: bio_bulletin_board@bioinformatics.org
List-Unsubscribe: <https://bioinformatics.org/mailman/listinfo/bio_bulletin_board>,
	<mailto:bio_bulletin_board-request@bioinformatics.org?subject=unsubscribe>
List-Id: A Bioinformatics.Org members' discussion forum <bio_bulletin_board.bioinformatics.org>
List-Post: <mailto:bio_bulletin_board@bioinformatics.org>
List-Help: <mailto:bio_bulletin_board-request@bioinformatics.org?subject=help>
List-Subscribe: <https://bioinformatics.org/mailman/listinfo/bio_bulletin_board>,
	<mailto:bio_bulletin_board-request@bioinformatics.org?subject=subscribe>
List-Archive: <https://bioinformatics.org/pipermail/bio_bulletin_board/>
Date: Fri,  6 Aug 2004 00:16:47 +0100

Hi all,

I have a question that concerns my MSc project. I am trying to cluster 30
CCP-modules (Complement Receptor 1) after having used a novel approach that
looks at the electrostatic surfaces. I have reached the stage where I have
obtained a similarity matrix of 30 by 30 filled with positive scores. The
higher a score the more similar two modules are. For example, if matrix entry
(3,6) = 13 and entry (3,8) = 24 then module 3 is more similar to module 8 than
to module 6 due to a higher score. My problem now is to cluster these 30
modules based on this one similarity matrix. I am not used to have to cluster
small datasets or in this case a similarity matrix and not having training
data. I have searched around a lot on Google for programs that could cluster my
modules using the similarity matrix but so far I have not found anything very
helpful. Does anyone know of a program (preferably free software) that could
help me out here, or another way which I could easily implement myself in a
script, that would be valid? I would really appreciate all replies to this
message and thank you all already for looking at this and thinking about this.

Thanks and regards,
Floris
_______________________________________________
BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board@bioinformatics.org
https://bioinformatics.org/mailman/listinfo/bio_bulletin_board

--------------060509080208070005030601--