smyRNA: A Novel Ab Initio ncRNA Gene Finder

Resource type
Date created
2009-05-05
Authors/Contributors
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
Document
Published as
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
Publication title
PLoS ONE
Document title
smyRNA: A Novel Ab Initio ncRNA Gene Finder
Date
2009
Volume
4
Issue
5
Publisher DOI
10.1371/journal.pone.0005433
Copyright statement
Copyright is held by the author(s).
Scholarly level
Peer reviewed?
Yes
Language
Member of collection
Attachment Size
Sahinalp-2009.pdf 350.78 KB