RSSVM (RNA Sampler + Support Vector Machine)

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When tested on a large number of known and random RNA motifs, RSSVM shows a significantly higher sensitivity than other leading RNA identification programs while maintaining the same false positive rate. RSSVM performs particularly well on sets with low sequence identities. The combination of RNA Sampler and RSSVM provides a new, fast and efficient pipeline for large-scale discovery of regulatory RNA motifs.

  

PDF reprint of the paper:

"Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines"

  


Xing Xu, Yongmei Ji, and Gary D. Stormo
Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines
PLoS Computational Biology, in revision, Sept 2008.


We applied RSSVM to multiple Shewanella genomes and identified putative regulatory RNA motifs in the 5กฏ-UTRs in S. oneidensis, an important bacterial organism with extraordinary respiratory and metal reducing abilities and great potentials for bioremediation. From 1002 sets of 5'-UTRs of orthologous operons, we identified 166 putative regulatory RNA motifs, including 17 of the 19 known RNA motifs from Rfam, additional 21 RNA motifs that are supported by literature evidence, 72 RNA motifs overlapping predicted transcription terminators or attenuators, and other candidate regulatory RNA motifs. Our study provides a list of promising novel regulatory RNA motifs potentially involved in post-transcriptional gene regulation. Combining with the previous cis-regulatory DNA motif study in S. oneidensis, this genome-wide discovery of cis-regulatory RNA motifs may offer more comprehensive views of gene regulation at a different level in this organism.

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We created a database, Shewanella cis-regulatory RNA element database,  for our prediction results.


If RSSVM is used in work that is published, please cite:
Xing Xu, Yongmei Ji, and Gary D. Stormo
Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines.

PLoS Comput Biol. 2009 Apr;5(4):e1000338. Epub 2009 Apr 3.


Please send bug reports, requests, comments and suggestions to  Xing Xu (xingxu AT genetics.wustl.edu), Yongmei Ji (yji AT genetics.wustl.edu) and Gary Stormo (stormo AT genetics.wustl.edu).


Unofficial version:

"Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines"

  

Supplementary materials: supplementary_material.tar 
Training sets: training_sets.tar 
Test sets: test_sets.tar 

Source code for the latest version:    RSSVM v1.0

RSSVM-v1.0.tar
RNAz-1.0_modified.tar
LIBSVM
RNASampler_v1.3.tar.gz

Instruction for installation and usage:    README.html

RNA Sampler development log:    updates


Last updated Sept 30, 2008