Blast2GO Revisited: State of the Art in Functional Annotation and Analysis of Non-Model Organisms

Next generation sequencing of genomes and transcriptomes poses new challenges to functional annotation pipelines both at the coverage as the throughput levels. Blast2GO is a state-of-the-art methodology for high-throughput functional annotation and analysis at genome scale and widely use among research related to non-model organisms. In this work we  overview established procedures for the functional annotation of sequence data and present new features of the latest Blast2GO release which has been reengineered to accelerate annotation turnover and improve data mining tasks. We provide insights into the relation between data coverage and quality i.e. the tradeoff between the percentage of genes/proteins with functional assignments and the quality of these assignments in terms of trustworthiness or reliability.