Nives Škunca

TL;DR: REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures.

TL;DR: Today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets, and there is considerable need for improvement of currently available tools.

TL;DR: The second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function, was conducted by as mentioned in this paper. But the results of the CAFA2 assessment are limited.

TL;DR: The second critical assessment of functional annotation (CAFA) conducted, a timed challenge to assess computational methods that automatically assign protein function, revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies.

TL;DR: Six major new developments in OMA are presented: a new web interface; Gene Ontology function predictions as part of the OMA pipeline; better support for plant genomes and in particular homeologs in the wheat genome; a new synteny viewer providing the genomic context of orthologs; statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format.