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2 Publications

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    Eddy/Rivas Lab
    05/15/09 | Infernal 1.0: inference of RNA alignments.
    Nawrocki EP, Kolbe DL, Eddy SR
    Bioinformatics. 2009 May 15;25:1335-7. doi: 10.1093/bioinformatics/btp157

    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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    Eddy/Rivas Lab
    05/15/09 | Local RNA structure alignment with incomplete sequence.
    Kolbe DL, Eddy SR
    Bioinformatics. 2009 May 15;25(10):1236-43. doi: 10.1093/bioinformatics/btp154

    Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing.

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