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. 2009 May 15;25(10):1335-7.
doi: 10.1093/bioinformatics/btp157. Epub 2009 Mar 23.

Infernal 1.0: inference of RNA alignments

Eric P Nawrocki  1 , Diana L Kolbe, Sean R Eddy
Affiliations

Infernal 1.0: inference of RNA alignments

Eric P Nawrocki et al. Bioinformatics. .

Erratum in

  • Bioinformatics. 2009 Jul 1;25(13):1713

Abstract

Summary: INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments.

Availability: Source code, documentation and benchmark 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.

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Figures

Fig. 1.
Fig. 1.
ROC curves for the benchmark. Plots are shown for the new infernal 1.0 with and without filters, for the old infernal 0.72 and for family-pairwise searches (FPS) with blastn. CPU times are total times for all 51 family searches measured for single execution threads on 3.0 GHz Intel Xeon processors. The infernal 1.0 times do not include time required for model calibration.
See this image and copyright information in PMC

References

    1. Altschul SF, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Brown MP. Small subunit ribosomal RNA modeling using stochastic context-free grammars. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2000;8:57–66. - PubMed
    1. Cole JR, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37:D141–D145. - PMC - PubMed
    1. Durbin R, et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press; 1998.
    1. Eddy SR. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics. 2002;3:18. - PMC - PubMed

Publication types