OrthoSearch: a scientific workflow approach to detect distant homologies on protozoans

Authors:
Sergio Manuel Serra da Cruz;Vanessa Batista;Alberto M. R. Dávila;Edno Silva;Frederico Tosta;Clarissa Vilela;Maria Luiza M. Campos;Rafael Cuadrat;Diogo Tschoeke;Marta Mattoso
Affiliations:
PESC/COPPE - UFRJ;PESC/COPPE - UFRJ;Oswaldo Cruz Institute - FIOCRUZ;PESC/COPPE - UFRJ;PESC/COPPE - UFRJ;PESC/COPPE - UFRJ;PPGI/IM/NCE - UFRJ;Oswaldo Cruz Institute - FIOCRUZ;Oswaldo Cruz Institute - FIOCRUZ;PESC/COPPE - UFRJ
Venue:
Proceedings of the 2008 ACM symposium on Applied computing
Year:
2008

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Abstract

Managing bioinformatics experiments is challenging due to the orchestration and interoperation of tools with semantics. An effective approach for managing those experiments is through workflow management systems (WfMS). We present several WfMS features for supporting genome homology workflows and discuss relevant issues for typical genomic experiments. In our evaluation we used OrthoSearch, a real genomic pipeline originally defined as a Perl script. We modeled it as a scientific workflow and implemented it on Kepler WfMS. We show a case study detecting distant homologies on trypanomatids metabolic pathways. Our results reinforce the benefits of WfMS over script languages and point out challenges to WfMS in distributed environments.