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A method to find groups of orthogous genes across multiple genomes

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Bibliographic Details
Main Author: Telles, Guilherme P.
Publication Date: 2013
Other Authors: Almeida Júnior, Nalvo Franco de, Alvarez, Paulo A., Brígido, Marcelo de Macedo, Walter, Maria Emília Machado Telles
Format: Article
Language: eng
Source: Repositório Institucional da UnB
Download full: http://repositorio.unb.br/handle/10482/32110
Summary: In this work we propose a simple method to obtain groups of homologous genes across multiple (k) organisms, called kGC. Our method takes as input all-against-all Blastp comparisons and produces groups of homologous sequences. First, homologies among groups of paralogs of all the k compared genomes are found, followed by homologies of groups among k - 1 genomes and so on, until groups belonging exclusively to only one genome, that is, groups of one genome not presenting strong similarities with any group of any other genome, are identified. We have used our method to determine homologous groups across six Actinobacterial complete genomes. To validate kGC, we first investigate the Pfam classification of the homologous groups, and after compare our results with those produced by OrthoMCL. Although kGC is much simpler than OrthoMCL it presented similar results with respect to Pfam classification.
Summary:In this work we propose a simple method to obtain groups of homologous genes across multiple (k) organisms, called kGC. Our method takes as input all-against-all Blastp comparisons and produces groups of homologous sequences. First, homologies among groups of paralogs of all the k compared genomes are found, followed by homologies of groups among k - 1 genomes and so on, until groups belonging exclusively to only one genome, that is, groups of one genome not presenting strong similarities with any group of any other genome, are identified. We have used our method to determine homologous groups across six Actinobacterial complete genomes. To validate kGC, we first investigate the Pfam classification of the homologous groups, and after compare our results with those produced by OrthoMCL. Although kGC is much simpler than OrthoMCL it presented similar results with respect to Pfam classification.

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