Nucleic Acids Research, 1994, Vol. 22, No. 11 2079-2088
© 1994
COMPUTATIONAL BIOLOGY |
RNA sequence analysis using covariance models
MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK
*To whom correspondence should be addressed
Received February 16, 1994. Revised April 26, 1994. Accepted April 26, 1994.
We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models ‘covariance models’. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA scondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. Jamalludeen, A. M. Kropinski, R. P. Johnson, E. Lingohr, J. Harel, and C. L. Gyles Complete Genomic Sequence of Bacteriophage {phi}EcoM-GJ1, a Novel Phage That Has Myovirus Morphology and a Podovirus-Like RNA Polymerase Appl. Envir. Microbiol., January 15, 2008; 74(2): 516 - 525. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Zaneveld, D. R. Nemergut, and R. Knight Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns Microbiology, January 1, 2008; 154(1): 1 - 15. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. M. Meyer A practical guide to the art of RNA gene prediction Brief Bioinform, November 1, 2007; 8(6): 396 - 414. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. S. Andersen, A. Lind-Thomsen, B. Knudsen, S. E. Kristensen, J. H. Havgaard, E. Torarinsson, N. Larsen, C. Zwieb, P. Sestoft, J. Kjems, et al. Semiautomated improvement of RNA alignments RNA, November 1, 2007; 13(11): 1850 - 1859. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Xu, Y. Ji, and G. D. Stormo RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment Bioinformatics, August 1, 2007; 23(15): 1883 - 1891. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Taquist, Y. Cui, and D. H. Ardell TFAM 1.0: an online tRNA function classifier Nucleic Acids Res., July 13, 2007; 35(suppl_2): W350 - W353. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Weinberg, J. E. Barrick, Z. Yao, A. Roth, J. N. Kim, J. Gore, J. X. Wang, E. R. Lee, K. F. Block, N. Sudarsan, et al. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline Nucleic Acids Res., July 9, 2007; (2007) gkm487v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. A. Davis, M. P. S. Brown, and U. Singh Functional Characterization of Spliceosomal Introns and Identification of U2, U4, and U5 snRNAs in the Deep-Branching Eukaryote Entamoeba histolytica Eukaryot. Cell, June 1, 2007; 6(6): 940 - 948. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Sugahara, N. Yachie, K. Arakawa, and M. Tomita In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs RNA, May 1, 2007; 13(5): 671 - 681. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Torarinsson, J. H. Havgaard, and J. Gorodkin Multiple structural alignment and clustering of RNA sequences Bioinformatics, April 15, 2007; 23(8): 926 - 932. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Kim, H. H. Gan, and T. Schlick A computational proposal for designing structured RNA pools for in vitro selection of RNAs RNA, April 1, 2007; 13(4): 478 - 492. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. St-Onge, P. Thibault, S. Hamel, and F. Major Modeling RNA tertiary structure motifs by graph-grammars Nucleic Acids Res., March 27, 2007; (2007) gkm069v2. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. K. Freyhult, J. P. Bollback, and P. P. Gardner Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA Genome Res., January 1, 2007; 17(1): 117 - 125. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Lindgreen, P. P. Gardner, and A. Krogh Measuring covariation in RNA alignments: physical realism improves information measures Bioinformatics, December 15, 2006; 22(24): 2988 - 2995. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hamada, K. Tsuda, T. Kudo, T. Kin, and K. Asai Mining frequent stem patterns from unaligned RNA sequences Bioinformatics, October 15, 2006; 22(20): 2480 - 2487. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Thebault, S. de Givry, T. Schiex, and C. Gaspin Searching RNA motifs and their intermolecular contacts with constraint networks Bioinformatics, September 1, 2006; 22(17): 2074 - 2080. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Withers, L. Wernisch, and M. d. Reis Archaeology and evolution of transfer RNA genes in the Escherichia coli genome RNA, June 1, 2006; 12(6): 933 - 942. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Yao, Z. Weinberg, and W. L. Ruzzo CMfinder--a covariance model based RNA motif finding algorithm Bioinformatics, February 15, 2006; 22(4): 445 - 452. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. H. Ardell and S. G. E. Andersson TFAM detects co-evolution of tRNA identity rules with lateral transfer of histidyl-tRNA synthetase Nucleic Acids Res., February 9, 2006; 34(3): 893 - 904. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Freyhult, V. Moulton, and D. H. Ardell Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos Nucleic Acids Res., February 9, 2006; 34(3): 905 - 916. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Weinberg and W. L. Ruzzo Sequence-based heuristics for faster annotation of non-coding RNA families Bioinformatics, January 1, 2006; 22(1): 35 - 39. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. SEKI and S. KOBAYASHI A Grammatical Approach to the Alignment of Structure-Annotated Strings IEICE Trans D: Information, December 1, 2005; E88-D(12): 2727 - 2737. [Abstract] [PDF]
|
|
|
|
 |
|
 I. Lopez de Silanes, S. Galban, J. L. Martindale, X. Yang, K. Mazan-Mamczarz, F. E. Indig, G. Falco, M. Zhan, and M. Gorospe Identification and Functional Outcome of mRNAs Associated with RNA-Binding Protein TIA-1 Mol. Cell. Biol., November 1, 2005; 25(21): 9520 - 9531. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. WOLF, M. ACHTZIGER, J. SCHULTZ, T. DANDEKAR, and T. MULLER Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures RNA, November 1, 2005; 11(11): 1616 - 1623. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. REN, B. RASTEGARI, A. CONDON, and H. H. HOOS HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots RNA, October 1, 2005; 11(10): 1494 - 1504. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Siebert and R. Backofen MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons Bioinformatics, August 15, 2005; 21(16): 3352 - 3359. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Piccinelli, M. A. Rosenblad, and T. Samuelsson Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes Nucleic Acids Res., August 8, 2005; 33(14): 4485 - 4495. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Schattner, A. N. Brooks, and T. M. Lowe The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs Nucleic Acids Res., July 1, 2005; 33(suppl_2): W686 - W689. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-W. Nam, K.-R. Shin, J. Han, Y. Lee, V. N. Kim, and B.-T. Zhang Human microRNA prediction through a probabilistic co-learning model of sequence and structure Nucleic Acids Res., June 24, 2005; 33(11): 3570 - 3581. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Matsui, K. Sato, and Y. Sakakibara Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures Bioinformatics, June 1, 2005; 21(11): 2611 - 2617. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Zhang and V. N. Gladyshev An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes Bioinformatics, June 1, 2005; 21(11): 2580 - 2589. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. E. BARRICK, N. SUDARSAN, Z. WEINBERG, W. L. RUZZO, and R. R. BREAKER 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter RNA, May 1, 2005; 11(5): 774 - 784. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Legendre, A. Lambert, and D. Gautheret Profile-based detection of microRNA precursors in animal genomes Bioinformatics, April 1, 2005; 21(7): 841 - 845. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Moulton Tracking down noncoding RNAs PNAS, February 15, 2005; 102(7): 2269 - 2270. [Full Text] [PDF]
|
|
|
|
|
|
C. ZWIEB, R. W. VAN NUES, M. A. ROSENBLAD, J. D. BROWN, and T. SAMUELSSON A nomenclature for all signal recognition particle RNAs RNA, January 1, 2005; 11(1): 7 - 13. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Rosenblad and T. Samuelsson Identification of Chloroplast Signal Recognition Particle RNA Genes Plant Cell Physiol., November 15, 2004; 45(11): 1633 - 1639. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. B. Lobocka, D. J. Rose, G. Plunkett III, M. Rusin, A. Samojedny, H. Lehnherr, M. B. Yarmolinsky, and F. R. Blattner Genome of Bacteriophage P1 J. Bacteriol., November 1, 2004; 186(21): 7032 - 7068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Pedersen, I. M. Meyer, R. Forsberg, P. Simmonds, and J. Hein A comparative method for finding and folding RNA secondary structures within protein-coding regions Nucleic Acids Res., September 24, 2004; 32(16): 4925 - 4936. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. KNIGHT, A. BIRMINGHAM, and M. YARUS BayesFold: Rational 2{degrees} folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences RNA, September 1, 2004; 10(9): 1323 - 1336. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Coventry, D. J. Kleitman, and B. Berger MSARI: Multiple sequence alignments for statistical detection of RNA secondary structure PNAS, August 17, 2004; 101(33): 12102 - 12107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Lambert, J.-F. Fontaine, M. Legendre, F. Leclerc, E. Permal, F. Major, H. Putzer, O. Delfour, B. Michot, and D. Gautheret The ERPIN server: an interface to profile-based RNA motif identification Nucleic Acids Res., July 1, 2004; 32(suppl_2): W160 - W165. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. L. de Silanes, M. Zhan, A. Lal, X. Yang, and M. Gorospe Identification of a target RNA motif for RNA-binding protein HuR PNAS, March 2, 2004; 101(9): 2987 - 2992. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Laslett and B. Canback ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences Nucleic Acids Res., January 2, 2004; 32(1): 11 - 16. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. VITRESCHAK, D. A. RODIONOV, A. A. MIRONOV, and M. S. GELFAND Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element RNA, September 1, 2003; 9(9): 1084 - 1097. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Peleg, E. N. Trifonov, and A. Bolshoy Hidden messages in the nef gene of human immunodeficiency virus type 1 suggest a novel RNA secondary structure Nucleic Acids Res., July 15, 2003; 31(14): 4192 - 4200. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-J. Hu GPRM: a genetic programming approach to finding common RNA secondary structure elements Nucleic Acids Res., July 1, 2003; 31(13): 3446 - 3449. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. TSUI, T. MACKE, and D. A. CASE A novel method for finding tRNA genes RNA, May 1, 2003; 9(5): 507 - 517. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Rosenblad, J. Gorodkin, B. Knudsen, C. Zwieb, and T. Samuelsson SRPDB: Signal Recognition Particle Database Nucleic Acids Res., January 1, 2003; 31(1): 363 - 364. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. R. Eddy Rfam: an RNA family database Nucleic Acids Res., January 1, 2003; 31(1): 439 - 441. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A. Rodionov, A. G. Vitreschak, A. A. Mironov, and M. S. Gelfand Comparative Genomics of Thiamin Biosynthesis in Procaryotes. NEW GENES AND REGULATORY MECHANISMS J. Biol. Chem., December 6, 2002; 277(50): 48949 - 48959. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y.-J. Hu Prediction of consensus structural motifs in a family of coregulated RNA sequences Nucleic Acids Res., September 1, 2002; 30(17): 3886 - 3893. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-Y. Le, K. Zhang, and J. V. Maizel Jr RNA molecules with structure dependent functions are uniquely folded Nucleic Acids Res., August 15, 2002; 30(16): 3574 - 3582. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Regalia, M. A. Rosenblad, and T. Samuelsson Prediction of signal recognition particle RNA genes Nucleic Acids Res., August 1, 2002; 30(15): 3368 - 3377. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. G. Vitreschak, D. A. Rodionov, A. A. Mironov, and M. S. Gelfand Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation Nucleic Acids Res., July 15, 2002; 30(14): 3141 - 3151. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
P. Schattner Searching for RNA genes using base-composition statistics Nucleic Acids Res., May 1, 2002; 30(9): 2076 - 2082. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. E. Allison, D. Angeles, N. Tran-Dinh, and N. K. Verma Complete Genomic Sequence of SfV, a Serotype-Converting Temperate Bacteriophage of Shigellaflexneri J. Bacteriol., April 1, 2002; 184(7): 1974 - 1987. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Gorodkin, S. L. Stricklin, and G. D. Stormo Discovering common stem-loop motifs in unaligned RNA sequences Nucleic Acids Res., May 15, 2001; 29(10): 2135 - 2144. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. V. Byl and A. M. Kropinski Sequence of the Genome of Salmonella Bacteriophage P22 J. Bacteriol., November 15, 2000; 182(22): 6472 - 6481. [Abstract] [Full Text]
|
|
|
|
|
|
A. M. Kropinski Sequence of the Genome of the Temperate, Serotype-Converting, Pseudomonas aeruginosa Bacteriophage D3 J. Bacteriol., November 1, 2000; 182(21): 6066 - 6074. [Abstract] [Full Text]
|
|
|
|
|
|
J.-H. Chen, S.-Y. Le, and J. V. Maizel Prediction of common secondary structures of RNAs: a genetic algorithm approach Nucleic Acids Res., February 15, 2000; 28(4): 991 - 999. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|