Big Data Supervised Pairwise Ortholog Detection in Yeasts [chapter]

Deborah Galpert Cañizares, Sara del Río García, Francisco Herrera, Evys Ancede Gallardo, Agostinho Antunes, Guillermin Agüero-Chapin
2017 Yeast - Industrial Applications  
Ortholog are genes in different species, evolving from a common ancestor. Ortholog detection is essential to study phylogenies and to predict the function of unknown genes. The scalability of gene (or protein) pairwise comparisons and that of the classification process constitutes a challenge due to the ever-increasing amount of sequenced genomes. Ortholog detection algorithms, just based on sequence similarity, tend to fail in classification, specifically, in Saccharomycete yeasts with rampant
more » ... paralogies and gene losses. In this book chapter, a new classification approach has been proposed based on the combination of pairwise similarity measures in a decision system that consider the extreme imbalance between ortholog and non-ortholog pairs. Some new gene pair similarity measures are defined based on protein physicochemical profiles, gene pair membership to conserved regions in related genomes, and protein lengths. The efficiency and scalability of the calculation of these measures are analyzed to propose its implementation for big data. In conclusion, evaluated supervised algorithms that manage big and imbalanced data showed high effectiveness in Saccharomycete yeast genomes.
doi:10.5772/intechopen.70479 fatcat:ohsspdtebzbnff46alosjlnmzu