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RNAz 2.0: improved noncoding RNA detection.

TitleRNAz 2.0: improved noncoding RNA detection.
Publication TypeJournal Article
Year of Publication2010
AuthorsGruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF
JournalPac Symp Biocomput
Pagination69-79
Date Published2010
ISSN2335-6936
KeywordsAlgorithms, Base Sequence, Computational Biology, Models, Genetic, Nucleic Acid Conformation, RNA Stability, RNA, Untranslated, Sequence Alignment, Sequence Analysis, RNA, Software, Thermodynamics
Abstract

RNAz is a widely used software package for de novo detection of structured noncoding RNAs in comparative genomics data. Four years of experience have not only demonstrated the applicability of the approach, but also helped us to identify limitations of the current implementation. RNAz 2.0 provides significant improvements in two respects: (1) The accuracy is increased by the systematic use of dinucleotide models. (2) Technical limitations of the previous version, such as the inability to handle alignments with more than six sequences, are overcome by increased training data and the usage of an entropy measure to represent sequence similarities. RNAz 2.0 shows a significantly lower false discovery rate on a dinucleotide background model than the previous version. Separate models for structural alignments provide an additional way to increase the predictive power. RNAz is open source software and can be obtained free of charge at: http://www.tbi.univie.ac.at/~wash/RNAz/

Alternate JournalPac Symp Biocomput
PubMed ID19908359