Towards detection of orthologues in sequence databases

Motivation: Numerous homologous sequences from diverse species can be retrieved fr-om databases using programs such as BLAST. However; due to multigene families, evolutionary relationship often cannot be easily determined and proper functional assignment becomes difficult. Thus, discrimination between orthologues and paralogues within BLAST output lists of homologous sequences becomes more and mole important. Result: We therefor-e developed a method that attempts to construct a reconciled tree fi-om a gene tl-ee of selected sequences and its corresponding phylogenetic ti-ee of the species involved (species tree). An interface on the Web is developed to enable users to analyse the BLAST result. BLAST outputs are par sed and, for the selected sequences, multiple alignments are constructed either globally or for local regions. Bootstrapped trees are returned and compared with the expected species tree. In cases of discrepancies, gene duplications air assumed and a reconciled tl ee is computed. The reconciled tree shows probable orthologues and paralogues as predicted.