Infernal 1.1: 100-fold faster RNA homology searches

TLDR

Infernal builds probabilistic profiles of RNA families, called covariance models, from structurally annotated multiple‑sequence alignments. Version 1.1 introduces a filter pipeline that uses accelerated profile HMMs and HMM‑banded CM alignment to search for new RNA family members and construct large alignments. The new pipeline achieves roughly 100‑fold speedup over the previous version and about 10,000‑fold over exhaustive non‑filtered CM searches. Source code, documentation, benchmarks, and contact information are freely available at http://infernal.janelia.org under the GNU GPLv3.

Abstract

Abstract Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches. Availability: Source code, documentation and the benchmark are downloadable from http://infernal.janelia.org. Infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Documentation includes a user’s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software. Contact: [e-mail]