COMER2: GPU-accelerated sensitive and specific homology searches.

ABSTRACT:

Summary

Searching for homology in the vast amount of sequence data has a particular emphasis on its speed. We present a completely rewritten version of the sensitive homology search method COMER based on alignment of protein sequence profiles, which is capable of searching big databases even on a lightweight laptop. By harnessing the power of CUDA-enabled graphics processing units, it is up to 20 times faster than HHsearch, a state-of-the-art method using vectorized instructions on modern CPUs.

Availability and implementation

COMER2 is cross-platform open-source software available at https://sourceforge.net/projects/comer2 and https://github.com/minmarg/comer2. It can be easily installed from source code or using stand-alone installers.

Contact

mindaugas.margelevicius

SUBMITTER: Margelevicius M 

PROVIDER: S-EPMC7267824 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature