Infernal 1.1: 100-fold faster RNA homology searches. 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 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.

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  1. Walter Costa, Maria Beatriz; Höner zu Siederdissen, Christian; Tulpan, Dan; Stadler, Peter F.; Nowick, Katja: Temporal ordering of substitutions in RNA evolution: uncovering the structural evolution of the Human Accelerated Region 1 (2018)
  2. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  3. Picardi, Ernesto (ed.): RNA bioinformatics (2015)
  4. Kasabov, Nikola (ed.): Springer handbook of bio-/neuro-informatics (2014)
  5. Herbig, Alexander; Nieselt, Kay: Nocornac: characterization of non-coding rnas in prokaryotes (2011) ioport
  6. Weinberg, Zasha; Breaker, Ronald R.: R2R - software to speed the depiction of aesthetic consensus RNA secondary structures (2011) ioport
  7. Brabrand, Claus; Giegerich, Robert; Møller, Anders: Analyzing ambiguity of context-free grammars (2010)
  8. Capriotti, Emidio; Martí-Renom, Marc A.: Quantifying the relationship between sequence and three-dimensional structure conservation in RNA (2010) ioport
  9. Xia, Fei; Dou, Yong; Zhou, Dan; Li, Xin: Fine-grained parallel RNA secondary structure prediction using SCFGs on FPGA (2010)
  10. Nawrocki, Eric P.; Kolbe, Diana L.; Eddy, Sean R.: Infernal 1.0: inference of RNA alignments (2009) ioport
  11. Nawrocki, Eric P.; Kolbe, Diana L.; Eddy, Sean R.: Infernal 1.0: inference of RNA alignments (2009) ioport