Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.

ABSTRACT: A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method. The performance of both approaches was assessed through functional comparison of 446 bacterial genomes sampled at different taxonomic levels. We show that protein domain architectures provide a fast and efficient alternative t

SUBMITTER: Koehorst JJ 

PROVIDER: S-EPMC5031134 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature