Benchmarking the next generation of homology inference tools

Conclusion: Profile methods are superior at inferring remote homologs but the difference in accuracy between methods is relatively small. PHMMER and CSBLAST stand out with the highest accuracy, yet still at a reasonable computational cost. Additionally, we show that less than 0.1% of Swiss-Prot protein pairs considered homologous by one database are considered non-homologous by another, implying that these classifications represent equivalent underlying biological phenomena, differing mostly in coverage and granularity. Availability and Implementation: Benchmark datasets and all scripts are placed at (http://sonnhammer.org/download/Homology_benchmark). Contact: forslund@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.
Source: Bioinformatics - Category: Bioinformatics Authors: Tags: SEQUENCE ANALYSIS Source Type: research