A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

@article{citeulike:1442662, abstract = {Noncoding RNAs (ncRNAs) are important functional RNAs that do not code for proteins. We present a highly efficient computational pipeline for discovering cis-regulatory ncRNA motifs de novo. The pipeline differs from previous methods in that it is structure-oriented, does not require a multiple-sequence alignment as input, and is capable of detecting RNA motifs with low sequence conservation. We also integrate RNA motif prediction with RNA homolog search, which improves the quality of the RNA motifs significantly. Here, we report the results of applying this pipeline to Firmicute bacteria. Our top-ranking motifs include most known Firmicute elements found in the RNA family database (Rfam). Comparing our motif models with Rfam\&\#39;s hand-curated motif models, we achieve high accuracy in both membership prediction and base-pair\&\#8211;level secondary structure prediction (at least 75\&\#37; average sensitivity and specificity on both tasks). Of the ncRNA candidates not in Rfam, we find compelling evidence that some of them are functional, and analyze several potential ribosomal protein leaders in depth.}, author = {Yao, Zizhen and Barrick, Jeffrey and Weinberg, Zasha and Neph, Shane and Breaker, Ronald and Tompa, Martin and Ruzzo, Walter L. }, citeulike-article-id = {1442662}, doi = {http://dx.doi.org/10.1371/journal.pcbi.0030126}, journal = {PLoS Computational Biology}, keywords = {algorithms, bioinformatics, genomics, mirna, prokaryotes}, month = {July}, number = {7}, pages = {e126+}, posted-at = {2007-10-16 19:42:47}, priority = {4}, title = {A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes}, url = {http://dx.doi.org/10.1371/journal.pcbi.0030126}, volume = {3}, year = {2007} }

TY - JOUR ID - citeulike:1442662 L3 - citeulike-article-id:1442662 TI - A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes JF - PLoS Computational Biology VL - 3 IS - 7 SP - e126 N2 - Noncoding RNAs (ncRNAs) are important functional RNAs that do not code for proteins. We present a highly efficient computational pipeline for discovering cis-regulatory ncRNA motifs de novo. The pipeline differs from previous methods in that it is structure-oriented, does not require a multiple-sequence alignment as input, and is capable of detecting RNA motifs with low sequence conservation. We also integrate RNA motif prediction with RNA homolog search, which improves the quality of the RNA motifs significantly. Here, we report the results of applying this pipeline to Firmicute bacteria. Our top-ranking motifs include most known Firmicute elements found in the RNA family database (Rfam). Comparing our motif models with Rfam's hand-curated motif models, we achieve high accuracy in both membership prediction and base-pair–level secondary structure prediction (at least 75% average sensitivity and specificity on both tasks). Of the ncRNA candidates not in Rfam, we find compelling evidence that some of them are functional, and analyze several potential ribosomal protein leaders in depth. KW - algorithms KW - bioinformatics KW - genomics KW - mirna KW - prokaryotes AU - Yao, Zizhen AU - Barrick, Jeffrey AU - Weinberg, Zasha AU - Neph, Shane AU - Breaker, Ronald AU - Tompa, Martin AU - Ruzzo, Walter PY - 2007/07/01/ UR - http://dx.doi.org/10.1371/journal.pcbi.0030126 ER -