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Progress in quickly finding orthologs as reciprocal best hits: comparing blast, last, diamond and MMseqs2

Abstract:

Background Finding orthologs remains an important bottleneck in comparative genomics analyses. While the authors of software for the quick comparison of protein sequences evaluate the speed of their software and compare their results against the most usual software for the task, it is not common for them to evaluate their software for more particular uses, such as finding orthologs as reciprocal best hits (RBH). Here we compared RBH results obtained using software that runs faster than blastp. Namely, lastal, diamond, and MMseqs2. Results We found that lastal required the least time to produce results. However, it yielded fewer results than any other program when comparing the proteins encoded by evolutionarily distant genomes. The program producing the most similar number of RBH to blastp was diamond ran with the “ultra-sensitive” option …