BLASTing proteomes, yielding phylogenies.
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.
Fuellen
Georg
G
Integrated Functional Genomics, IZKF, University Hospital Münster (Hautklinik), Germany. fuellen@uni-muenster.de
Spitzer
Michael
M
Cullen
Paul
P
Lorkowski
Stefan
S
D000070998:ATP Binding Cassette Transporter, Subfamily G, Member 1; D018528:ATP-Binding Cassette Transporters / Q000235:genetics; D000465:Algorithms; D019295:Computational Biology; D016208:Databases, Factual; D019143:Evolution, Molecular; D006801:Humans; D010802:Phylogeny; D020543:Proteome / Q000235:genetics*; D012986:Software Validation
C419353:ABCG1 protein, human; D000070998:ATP Binding Cassette Transporter, Subfamily G, Member 1; D018528:ATP-Binding Cassette Transporters; D020543:Proteome