Benchmarking the next generation of homology inference tools.

ABSTRACT:

Motivation

Over the last decades, vast numbers of sequences were deposited in public databases. Bioinformatics tools allow homology and consequently functional inference for these sequences. New profile-based homology search tools have been introduced, allowing reliable detection of remote homologs, but have not been systematically benchmarked. To provide such a comparison, which can guide bioinformatics workflows, we extend and apply our previously developed benchmark approach to evaluate the 'next generation' of profile-based approaches, including CS-BLAST, HHSEARCH and PHMMER, in comparison with the non-profile based search tools NCBI-BLAST, USEARCH, UBLAST and FASTA.

Method

We generated challenging benchmark datasets based on protein domain architectures within either th

SUBMITTER: Saripella GV 

PROVIDER: S-EPMC5013910 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature