- Communication -

Volume 3

Full article

BLASTing proteomes, yielding phylogenies

Georg Fuellen^1,*, Michael Spitzer¹, Paul Cullen² and Stefan Lorkowski³

¹ Integrated Functional Genomics, IZKF, University Hospital Münster (Hautklinik), Von-Esmach-Str. 56, 48149 Münster, Germany
   Email: fuellen@uni-muenster.de, spitzem@uni-muenster.de
² Ogham GmbH, Mendelstr. 11, 48149 Münster, Germany
   Email: cullen@ogham.de
³ MAFAPS Research Group, Institute of Arteriosclerosis Research, Domagkstr. 3, 48149 Münster, Germany
   Email: stefan.lorkowski@uni-muenster.de

^*  corresponding author


Edited by E. Wingender; received October 04, 2002; revised March 03, 2003; accepted May 07, 2003; published May 24, 2003

Abstract

We develop a procedure called RiPE (Retrieval-induced Phylogeny Environment) that automatically performs an evolutionary analysis of a protein (sub)family, (i) by retrieving the relevant sequences via a homology search, (ii) by using the search report to construct the alignment using only homologous subsequences (taking into account their neighborhood with a low chance of homology), (iii) by realigning, and (iv) by generating phylogenetic trees based on the alignment. In a first implementation of our scheme, we start with the available proteome data of model organisms, perform a PSI-BLAST search, use MView to convert hits into a multiple alignment, and perform realignment and tree building. As a test case, we have investigated the human ABC transporters of the subfamily G, starting with the five known human ABCG transporters. Our method retrieved homologous sequences not previously analyzed, generating a tree that is more plausible and better supported than previously published trees. The RiPE 0.1 prototype is available at the RiPE website, http://ifg-izkf.uni-muenster.de/fuellen/RiPE/ripe.html.

Key words: mABC transporters, phylogeny, evolution, multiple alignment, homology search