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Bioinformatics Advance Access originally published online on February 15, 2005
Bioinformatics 2005 21(11):2596-2603; doi:10.1093/bioinformatics/bti325
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases

Jean-François Dufayard 1, Laurent Duret 2, Simon Penel 2, Manolo Gouy 2, François Rechenmann 1 and Guy Perrière 2,*

1INRIA Rhône-Alpes 38334 Montbonnot, Saint Ismier Cedex, France
2Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard—Lyon 1 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France

*To whom correspondence should be addressed.

Motivation: Comparative sequence analysis is widely used to study genome function and evolution. This approach first requires the identification of homologous genes and then the interpretation of their homology relationships (orthology or paralogy). To provide help in this complex task, we developed three databases of homologous genes containing sequences, multiple alignments and phylogenetic trees: HOBACGEN, HOVERGEN and HOGENOM. In this paper, we present two new tools for automating the search for orthologs or paralogs in these databases.

Results: First, we have developed and implemented an algorithm to infer speciation and duplication events by comparison of gene and species trees (tree reconciliation). Second, we have developed a general method to search in our databases the gene families for which the tree topology matches a peculiar tree pattern. This algorithm of unordered tree pattern matching has been implemented in the FamFetch graphical interface. With the help of a graphical editor, the user can specify the topology of the tree pattern, and set constraints on its nodes and leaves. Then, this pattern is compared with all the phylogenetic trees of the database, to retrieve the families in which one or several occurrences of this pattern are found. By specifying ad hoc patterns, it is therefore possible to identify orthologs in our databases.

Availability: The tree reconciliation program and the FamFetch interface are available from the Pôle Bioinformatique Lyonnais Web server at the following addresses: http://pbil.univ-lyon1.fr/software/RAP/RAP.htm and http://pbil.univ-lyon1.fr/software/famfetch.html

Contact: perriere{at}biomserv.univ-lyon1.fr


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