creators_name: Kumar, Manish
creators_name: Thakur, Varun
creators_name: Raghava, G.P.S.
type: article
datestamp: 2012-01-10 08:05:31
lastmod: 2012-01-10 08:05:31
metadata_visibility: show
title: COPid: composition based protein identification.
ispublished: pub
subjects: QR
full_text_status: public
note: OPEN ACCESS
abstract: In the past, a large number of methods have been developed for predicting various characteristics of a protein from its composition. In order to exploit the full potential of protein composition, we developed the web-server COPid to assist the researchers in annotating the function of a protein from its composition using whole or part of the protein. COPid has three modules called search, composition and analysis. The search module allows searching of protein sequences in six different databases. Search results list database proteins in ascending order of Euclidian distance or descending order of compositional similarity with the query sequence. The composition module allows calculation of the composition of a sequence and average composition of a group of sequences. The composition module also allows computing composition of various types of amino acids (e.g. charge, polar, hydrophobic residues). The analysis module provides the following options; i) comparing composition of two classes of proteins, ii) creating a phylogenetic tree based on the composition and iii) generating input patterns for machine learning techniques. We have evaluated the performance of composition-based (or alignment-free) similarity search in the subcellular localization of proteins. It was found that the alignment free method performs reasonably well in predicting certain classes of proteins. The COPid web-server is available at http://www.imtech.res.in/raghava/copid/.
date: 2008
date_type: published
publication: In silico biology
volume: 8
number: 2
publisher: Bioinformation Systems e.V.   
pagerange: 121-8
refereed: TRUE
issn: 1386-6338
official_url: http://www.bioinfo.de/isb/2008/08/0011/
related_url_url: http://www.imtech.res.in/raghava/copid/
related_url_type: author
citation:   Kumar, Manish and Thakur, Varun and Raghava, G.P.S.  (2008) COPid: composition based protein identification.  In silico biology, 8 (2).  pp. 121-8.  ISSN 1386-6338     
document_url: http://crdd.osdd.net/open/45/1/raghava2008.mht