RNA Gene Prediction


The rapid growth of sequenced genomes and the discovery of numerous novel RNA species has made the development of methods for the computational identification of genes encoding functional RNA a high priority. Recent developments of algorithms for RNA gene prediction are based on diverse criteria, including location of promoters and terminators, sequence conservation among related genomes, RNA baseā€pairing and nucleotide composition.

Keywords: functional RNA; gene finding; genomics; bioinformatics; machine learning

Figure 1.

Comparison of RNA and protein genes in prokaryotes. In the RNA gene, there are no ribosome binding sites, no start or stop codons, and no triplet code.



Argaman L, Hershberg R, Vogel J, et al. (2001) Novel small RNA‐encoding genes in the intergenic regions of Escherichia coli. Current Biology 11: 941–950.

Carter RJ, Dubchak I and Holbrook SR (2001) A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Research 29(19): 3928–3938.

Eddy SR and Durbin R (1994) RNA sequence analysis using covariance models. Nucleic Acids Research 22: 2079–2088.

Huttenhofer A, Kiefmann M, Meier‐Ewert S, et al. (2001) RNomics: an experimental approach that identifies 201 candidates for novel, small, non‐messenger RNAs in mouse. EMBO Journal 20: 2943–2953.

Lau NC, Lim LP, Weinstein EG and Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858–862.

Lesnik EA, Sampath R, Levene HB, et al. (2001) Prediction of rho‐independent transcriptional terminators in Escherichia coli. Nucleic Acids Research 29: 3583–3594.

Lowe T and Eddy SR (1997) tRNAscan‐SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25: 955–964.

Lowe TM and Eddy SR (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283: 1168–1171.

Olivas WM, Muhlrad D and Parker R (1997) Analysis of the yeast genome: identification of new non‐coding and small ORF‐containing RNAs. Nucleic Acids Research 25: 4619–4625.

Omer AD, Lowe TM, Russell AG, et al. (2000) Homologues of snoRNAs in Archaea. Science 288: 517–522.

Rivas E, Klein RJ, Jones TA and Eddy SR (2001) Computational identification of noncoding RNAs in E. coli by comparative genomics. Current Biology 11: 1369–1373.

Ruvkin G (2001) Glimpses of a tiny RNA world. Science 294: 797–799.

Schattner P (2002) Searching for RNA genes using base‐composition statistics. Nucleic Acids Research 30: 2076–2082.

Wassarman KM, Repoila F, Rosenow C, Storz G and Gottesman S (2001) Identification of novel small RNAs using comparative genomics and microarrays. Genes and Development 15: 1637–1651.

Further Reading

Chen S et al. (2002) A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. BioSystems 65: 157–177.

Eddy SR (2001) Non‐coding RNA genes and the modern RNA world. Nature Reviews Genetics 2: 919–929.

Eddy SR (2002) Computational genomics of noncoding RNA genes. Cell 109: 137–140.

Laslett D, Canback B and Andersson S (2002) BRUCE: a program for the detection of transfer‐messenger RNA genes in nucleotide sequences. Nucleic Acids Research 30: 3449–3453.

Regalia M, Rosenblad MA and Samuelsson T (2002) Prediction of signal recognition particle RNA genes. Nucleic Acids Research 30: 3368–3377.

Storz G (2002) An expanding universe of noncoding RNAs. Science 296: 1260–1263.

Szymanski M and Barciszewski J (2002) Beyond the proteome: non‐coding regulatory RNAs. Genome Biology 1–8.

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Holbrook, Stephen R, Carter, Richard J, and Meraz, Richard F(Sep 2005) RNA Gene Prediction. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005271]