- Article -
| In Silico Biology 6, 0004 (2006); ©2005, Bioinformation Systems e.V. |
Hunting for insect-specific protein domains
Daniel R. Matute1, Emiliano Barreto-Hernandez2 and Laurent Falquet3*
1 Universidad Los Andes, Carrera 1 N° 18A - 10 Bogotá, Colombia
2 Instituto de Biotecnología, Universidad Nacional de Colombia, Bogotá, Colombia
3 Swiss Institute of Bioinformatics, UNIL-BEP, CH-1015 Lausanne, Switzerland
* Corresponding author
Email: Laurent.Falquet@isb-sib.ch; Phone: +41-21-6924078
Edited by H. Michael; received August 18, 2005; revised and accepted December 13, 2005; published January 03, 2006
Abstract
Automatically finding new protein domains is a challenge when using the complete collection of known proteins (i. e., UniProt). By limiting the taxonomic range to class insecta, including two full proteomes (A. gambiae and D. melanogaster), we reduced the size of the search space in the hope of finding taxon-specific domains. The MKDOM2 program (http://prodes.toulouse.inra.fr/prodom/xdom/mkdom2.html) was used to cluster the insect proteins into potential domains that were analyzed manually in a second step. We analyzed 219 potential domains, of which 2 were insect-specific. We show that it is possible to find new domains or to extend known domains using a semi-automated method; however the goal to detect class-specific domains was only partially achieved in the sense that the new domains we found were not all insect-specific domains.
The files used as input and the resulting output files, as well as extensive descriptions of the domains, are available as supplementary data from http://bioinf.ibun.unal.edu.co/insecta/.
Keywords: domains, insect, ProDom, Prosite, HMM, MKDOM