publication . Article . Other literature type . 2012

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

Rolf Backofen; Sebastian Will; Tejal Joshi; Peter F. Stadler; Ivo L. Hofacker;

Open Access

Published: 26 Mar 2012

Summary
Related research

Abstract

Current genomic screens for noncoding RNAs (ncRNAs) predict a large number of genomic regions containing potential structural ncRNAs. The analysis of these data requires highly accurate prediction of ncRNA boundaries and discrimination of promising candidate ncRNAs from weak predictions. Existing methods struggle with these goals because they rely on sequencebased multiple sequence alignments, which regularly misalign RNA structure and therefore do not support identification of structural similarities. To overcome this limitation, we compute columnwise and global reliabilities of alignments based on sequence and structure similarity; we refer to these structure-...

doi: 10.1261/rna.029041.111

pmid: 22450757

pmc: PMC3334699

Subjects

free text keywords: boundary prediction, columnwise reliability, global reliability, Primates Mammalia Vertebrata Chordata Animalia (Animals, Chordates, Humans, Mammals, Primates, Vertebrates) - Hominidae [86215] human common, human ncRNA gene [Hominidae], noncoding RNA ncRNA, 00530, General biology - Information, documentation, retrieval and computer applications, 03502, Genetics - General, 03508, Genetics - Human, 04500, Mathematical biology and statistical methods, Biochemistry and Molecular Biophysics, Computational Biology, LocARNA-P computer software, sequence-structure-based alignment reliability STAR mathematical and computer techniques, Computer Applications, Mathematical Biology, Molecular Genetics, de novo prediction of RNA, reliability of structural alignment, simultaneous alignment and folding, Sequence alignment, Nucleic acid structure, Non-coding RNA, Bioinformatics, Ncrna gene, Software tool, Software package, Biology, Software, business.industry, business

Related Organizations