Affiliations: Universidad Los Andes, Carrera 1 N° 18A – 10
Bogotá, Colombia | Instituto de Biotecnología, Universidad
Nacional de Colombia, Bogotá, Colombia | Swiss Institute of Bioinformatics, UNIL-BEP, CH-1015
Lausanne, Switzerland
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/.
