Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (276K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (69)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Carter, R. J.
Right arrow Articles by Holbrook, S. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Carter, R. J.
Right arrow Articles by Holbrook, S. R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2001, Vol. 29, No. 19 3928-3938
© 2001 Oxford University Press

A computational approach to identify genes for functional RNAs in genomic sequences

Richard J. Carter, Inna Dubchak1 and Stephen R. Holbrook*

Computational and Theoretical Biology Department, Physical Biosciences Division and 1National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA

Currently there is no successful computational approach for identification of genes encoding novel functional RNAs (fRNAs) in genomic sequences. We have developed a machine learning approach using neural networks and support vector machines to extract common features among known RNAs for prediction of new RNA genes in the unannotated regions of prokaryotic and archaeal genomes. The Escherichia coli genome was used for development, but we have applied this method to several other bacterial and archaeal genomes. Networks based on nucleotide composition were 80–90% accurate in jackknife testing experiments for bacteria and 90–99% for hyperthermophilic archaea. We also achieved a significant improvement in accuracy by combining these predictions with those obtained using a second set of parameters consisting of known RNA sequence motifs and the calculated free energy of folding. Several known fRNAs not included in the training datasets were identified as well as several hundred predicted novel RNAs. These studies indicate that there are many unidentified RNAs in simple genomes that can be predicted computationally as a precursor to experimental study. Public access to our RNA gene predictions and an interface for user predictions is available via the web.

* To whom correspondence should be addressed. Tel: +1 510 486 4305; Fax: +1 510 486 6059; Email: srholbrook{at}lbl.gov


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
T. T. Tran, F. Zhou, S. Marshburn, M. Stead, S. R. Kushner, and Y. Xu
De novo computational prediction of non-coding RNA genes in prokaryotic genomes
Bioinformatics, November 15, 2009; 25(22): 2897 - 2905.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. S. Shavkunov, I. S. Masulis, M. N. Tutukina, A. A. Deev, and O. N. Ozoline
Gains and unexpected lessons from genome-scale promoter mapping
Nucleic Acids Res., August 1, 2009; 37(15): 4919 - 4931.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
K. L. Smollett, A. S. Fivian-Hughes, J. E. Smith, A. Chang, T. Rao, and E. O. Davis
Experimental determination of translational start sites resolves uncertainties in genomic open reading frame predictions - application to Mycobacterium tuberculosis
Microbiology, January 1, 2009; 155(1): 186 - 197.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Pichon and B. Felden
Small RNA gene identification and mRNA target predictions in bacteria
Bioinformatics, December 15, 2008; 24(24): 2807 - 2813.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. T. Tran, P. Dam, Z. Su, F. L. Poole II, M. W. W. Adams, G. T. Zhou, and Y. Xu
Operon prediction in Pyrococcus furiosus
Nucleic Acids Res., January 12, 2007; 35(1): 11 - 20.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Wang, C. Ding, R. F. Meraz, and S. R. Holbrook
PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
Bioinformatics, November 1, 2006; 22(21): 2590 - 2596.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
J. K. Christiansen, J. S. Nielsen, T. Ebersbach, P. Valentin-Hansen, L. Sogaard-Andersen, and B. H. Kallipolitis
Identification of small Hfq-binding RNAs in Listeria monocytogenes
RNA, July 1, 2006; 12(7): 1383 - 1396.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
H. Ochman and L. M. Davalos
The nature and dynamics of bacterial genomes.
Science, March 24, 2006; 311(5768): 1730 - 1733.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
P. Larranaga, B. Calvo, R. Santana, C. Bielza, J. Galdiano, I. Inza, J. A. Lozano, R. Armananzas, G. Santafe, A. Perez, et al.
Machine learning in bioinformatics
Brief Bioinform, March 1, 2006; 7(1): 86 - 112.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
U. Laserson, H. H. Gan, and T. Schlick
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs
Nucleic Acids Res., October 27, 2005; 33(18): 6057 - 6069.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Saetrom, R. Sneve, K. I. Kristiansen, O. Snove Jr, T. Grunfeld, T. Rognes, and E. Seeberg
Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming
Nucleic Acids Res., June 7, 2005; 33(10): 3263 - 3270.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Pasquali, H. H. Gan, and T. Schlick
Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs
Nucleic Acids Res., March 3, 2005; 33(4): 1384 - 1398.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Vogel, V. Bartels, T. H. Tang, G. Churakov, J. G. Slagter-Jager, A. Huttenhofer, and E. G. H. Wagner
RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
Nucleic Acids Res., November 15, 2003; 31(22): 6435 - 6443.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. P. McCutcheon and S. R. Eddy
Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics
Nucleic Acids Res., July 15, 2003; 31(14): 4119 - 4128.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. H. Gan, S. Pasquali, and T. Schlick
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
Nucleic Acids Res., June 1, 2003; 31(11): 2926 - 2943.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
H. Kiyosawa, I. Yamanaka, N. Osato, S. Kondo, and Y. Hayashizaki
Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation
Genome Res., June 1, 2003; 13(6): 1324 - 1334.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Hershberg, S. Altuvia, and H. Margalit
A survey of small RNA-encoding genes in Escherichia coli
Nucleic Acids Res., April 1, 2003; 31(7): 1813 - 1820.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. Szymanski, V. A. Erdmann, and J. Barciszewski
Noncoding regulatory RNAs database
Nucleic Acids Res., January 1, 2003; 31(1): 429 - 431.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Tjaden, R. M. Saxena, S. Stolyar, D. R. Haynor, E. Kolker, and C. Rosenow
Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays
Nucleic Acids Res., September 1, 2002; 30(17): 3732 - 3738.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H.-c. Wang and D. A. Hickey
Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes
Nucleic Acids Res., June 1, 2002; 30(11): 2501 - 2507.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. J. Klein, Z. Misulovin, and S. R. Eddy
Noncoding RNA genes identified in AT-rich hyperthermophiles
PNAS, May 28, 2002; 99(11): 7542 - 7547.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
G. Storz
An Expanding Universe of Noncoding RNAs
Science, May 17, 2002; 296(5571): 1260 - 1263.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
N. J. Kaplinsky, D. M. Braun, J. Penterman, S. A. Goff, and M. Freeling
Utility and distribution of conserved noncoding sequences in the grasses
PNAS, April 30, 2002; 99(9): 6147 - 6151.
[Abstract] [Full Text] [PDF]

Home page
 Cold Spring Harb Symp Quant BiolHome page
S. GOTTESMAN, G. STORZ, C. ROSENOW, N. MAJDALANI, F. REPOILA, and K.M. WASSARMAN
Small RNA Regulators of Translation: Mechanisms of Action and Approaches for Identifying New Small RNAs
Cold Spring Harb Symp Quant Biol, January 1, 2001; 66(0): 353 - 362.
[Abstract] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
N. J. Kaplinsky, D. M. Braun, J. Penterman, S. A. Goff, and M. Freeling
Utility and distribution of conserved noncoding sequences in the grasses
PNAS, April 30, 2002; 99(9): 6147 - 6151.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.