Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing. Export

@article{citeulike:3293050, abstract = {MOTIVATION: 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. RESULTS: 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. AVAILABILITY: Stemloc-AMA is available from http://biowiki.org/StemLocAMA as part of the dart software package for sequence analysis. CONTACT: lpachter@math.berkeley.edu, ihh@berkeley.edu.}, address = {Biophysics Graduate Group, Department of Mathematics and Department of Bioengineering, University of California, Berkeley, CA 94720, USA.}, author = {Bradley, Robert K K. and Pachter, Lior and Holmes, Ian}, citeulike-article-id = {3293050}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btn495}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/23/2677}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18796475}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18796475}, day = {16}, doi = {10.1093/bioinformatics/btn495}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {alignment, ncrna}, month = {September}, posted-at = {2008-11-21 12:20:13}, priority = {2}, title = {Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing.}, url = {http://dx.doi.org/10.1093/bioinformatics/btn495}, year = {2008} }

TY - JOUR ID - citeulike:3293050 L3 - citeulike-article-id:3293050 N2 - MOTIVATION: 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. RESULTS: 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. AVAILABILITY: Stemloc-AMA is available from http://biowiki.org/StemLocAMA as part of the dart software package for sequence analysis. CONTACT: lpachter@math.berkeley.edu, ihh@berkeley.edu. JF - Bioinformatics (Oxford, England) SN - 1460-2059 AD - Biophysics Graduate Group, Department of Mathematics and Department of Bioengineering, University of California, Berkeley, CA 94720, USA. TI - Specific Alignment of Structured RNA: Stochastic Grammars and Sequence Annealing. KW - alignment KW - ncrna AU - Bradley, Robert K AU - Pachter, Lior AU - Holmes, Ian PY - 2008/09/16/ UR - http://dx.doi.org/10.1093/bioinformatics/btn495 ER -