smyRNA: A Novel Ab Initio ncRNA Gene Finder

Peer reviewed: 
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Faculty/Staff
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Salari R, Aksay C, Karakoc E, Unrau PJ, Hajirasouliha I, et al. (2009) smyRNA: A Novel Ab Initio ncRNA Gene Finder. PLoS ONE 4(5): e5433. doi:10.1371/journal.pone.0005433

Date created: 
2009-05-05
Keywords: 
Non-coding RNAs
Ab initio ncRNA gene finder
Genome sequences
Abstract: 

Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs.Methodology/Principal FindingsWe present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences.Conclusions/SignificanceOur method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown) ncRNA families. Availability: http://compbio.cs.sfu.ca/taverna/smyrna

Language: 
English
Document type: 
Article
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Sponsor(s): 
NSERC
CRC Program
CFI
MITACS
MSFHR
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