COPid: Composition Based Protein Identification

Article type: Research Article

Authors: Kumar, Manish | Thakur, Varun | Raghava, Gajendra P.S.

Affiliations: Institute of Microbial Technology, Sector 39-A, Chandigarh, India

Note: [] Corresponding author. Tel.: +91 172 2690557; Fax: +91 172 2690632; E-mail: [email protected]

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/.

Keywords: Compositional biasness, alignment-free similarity search, composition-based phylogenetic tree, residue composition, dipeptide composition

Journal: In Silico Biology, vol. 8, no. 2, pp. 121-128, 2008