Introduction

Whole-genome screens suggest that eukaryotic genomes are dense with non-coding RNAs (ncRNAs). We introduce a novel approach to RNA multiple alignment which couples a generative probabilistic model of sequence and structure with an efficient sequence annealing approach for exploring the space of multiple alignments. This leads to a new software program, Stemloc-AMA, that is both accurate and specific in the alignment of multiple related RNA sequences.When tested on the benchmark datasets BRalibase II and BRalibase 2.1, Stemloc-AMA has comparable sensitivity to and better specificity than the best competing methods. We use a large-scale random sequence experiment to show that while most alignment programs maximize sensitivity at the expense of specificity, even to the point of giving complete alignments of non-homologous sequences, Stemloc-AMA aligns only sequences with detectable homology and leaves unrelated sequences largely unaligned. Such accurate and specific alignments are crucial for comparative-genomics analysis, from inferring phylogeny to estimating substitution rates across different lineages.Stemloc-AMA is available from http://biowiki.org/StemLocAMA as part of the dart software package for sequence analysis.

Publications

  1. Specific alignment of structured RNA: stochastic grammars and sequence annealing.
    Cite this
    Bradley RK, Pachter L, Holmes I, 2008-12-01 - Bioinformatics (Oxford, England)

Credits

  1. Robert K Bradley
    Developer

    Biophysics Graduate Group, Department of Mathematics and Department of Bioengineering, United States of America

  2. Lior Pachter
    Developer

  3. Ian Holmes
    Investigator

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Summary
AccessionBT006604
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByIan Holmes