Journal
BIOINFORMATICS
Volume 29, Issue 22, Pages 2933-2935Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btt509
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Funding
- Howard Hughes Medical Institute
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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 similar to 100-fold acceleration over the previous version and similar to 10 000-fold acceleration over exhaustive non-filtered CM searches.
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