MMseqs2: sensitive protein sequence searching for the analysis of massive data sets

Sequencing costs have dropped much faster than Moores law in the past decade, and sensitive sequence searching has become the main bottleneck in the analysis of large metagenomic datasets. We therefore developed the open-source software MMseqs2 (mmseqs.org), which improves on current search tools over the full range of speed-sensitivity trade-off, achieving sensitivities better than PSI-BLAST at more than 400 times its speed.