GeM-Pro: A tool for genome functional mining and microbial profiling

TORRES MANNO, MARIANO A.; PIZARRO, DOLORES M.; PRUNELLO, MARCOS; MAGNI, CHRISTIAN; DAURELIO, LUCAS D.; ESPARIZ, MARTIN

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

SPRINGER

Lugar: Berlin; Año: 2019 vol. 103 p. 3123 - 3134

0175-7598

Gem-Pro is a newtool for gene mining and functional profiling of bacteria. It initially identifieshomologous genes using BLAST and then applies three filtering steps to selectorthologous gene pairs. The first one uses BLAST score values to identifytrivial paralogues. The second filter uses the shared identity percentages of foundtrivial paralogues as internal witnesses of non-orthology to set orthologycut-off values. The third filtering step uses conditional probabilities oforthology and non-orthology to define new cut-offs and generate supportiveinformation of orthology assignations. Additionally, a subsidiary tool, called q-GeM,was also developed to mine traits of interest using logistic regression (LR) orlinear discriminant analysis (LDA) classifiers. q-GeM is more efficient in theuse of computing resources than Gem-Pro but needs an initial classified set of homologousgenes in order to train LR and LDA classifiers. Hence, q-GeM could be used toanalyse new set of strains with available genome sequences, without the need torerun a complete Gem-Pro analysis. Finally, Gem-Pro and q-GeM perform a syntenyanalysis to evaluate the integrity and genomic arrangement of specific pathwaysof interest to infer their presence. The tools were applied to more than 2million homologous pairs encoded by Bacillusstrains generating statistical supported predictions of trait contents. Thedifferent patterns of encoded traits of interest were successfully used toperform a descriptive bacterial profiling.