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Noncoding RNA gene detection using comparative sequence analysis.

Rivas E, Eddy SR.

BMC Bioinformatics. 2001;2:8. Epub 2001 Oct 10.PMID: 11801179 [PubMed - indexed for MEDLINE]Related articlesFree article

Pair hidden Markov models on tree structures.

Sakakibara Y.

Bioinformatics. 2003;19 Suppl 1:i232-40.PMID: 12855464 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational identification of noncoding RNAs in E. coli by comparative genomics.

Rivas E, Klein RJ, Jones TA, Eddy SR.

Curr Biol. 2001 Sep 4;11(17):1369-73.PMID: 11553332 [PubMed - indexed for MEDLINE]Related articles

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

Matsui H, Sato K, Sakakibara Y.

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Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.

Uzilov AV, Keegan JM, Mathews DH.

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Evolutionary models for insertions and deletions in a probabilistic modeling framework.

Rivas E.

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Accelerated probabilistic inference of RNA structure evolution.

Holmes I.

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Prediction of small, noncoding RNAs in bacteria using heterogeneous data.

Tjaden B.

J Math Biol. 2008 Jan;56(1-2):183-200. Epub 2007 Mar 13.PMID: 17354017 [PubMed - indexed for MEDLINE]Related articles

ddbRNA: detection of conserved secondary structures in multiple alignments.

di Bernardo D, Down T, Hubbard T.

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Benchmarking tools for the alignment of functional noncoding DNA.

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB.

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Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.

Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB.

RNA. 2004 Sep;10(9):1309-22.PMID: 15317971 [PubMed - indexed for MEDLINE]Related articlesFree article

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures.

Matsui H, Sato K, Sakakibara Y.

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The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH.

PLoS Biol. 2003 Nov;1(2):E45. Epub 2003 Nov 17.PMID: 14624247 [PubMed - indexed for MEDLINE]Related articlesFree article

A grammar based methodology for structural motif finding in ncRNA database search.

Quest D, Tapprich W, Ali H.

Comput Syst Bioinformatics Conf. 2007;6:215-25.PMID: 17951826 [PubMed - indexed for MEDLINE]Related articlesFree article

Considerations in the identification of functional RNA structural elements in genomic alignments.

Babak T, Blencowe BJ, Hughes TR.

BMC Bioinformatics. 2007 Jan 30;8:33.PMID: 17263882 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolutionary triplet models of structured RNA.

Bradley RK, Holmes I.

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Dinucleotide controlled null models for comparative RNA gene prediction.

Gesell T, Washietl S.

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Specific alignment of structured RNA: stochastic grammars and sequence annealing.

Bradley RK, Pachter L, Holmes I.

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GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Besemer J, Lomsadze A, Borodovsky M.

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Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome.

Coenye T, Drevinek P, Mahenthiralingam E, Shah SA, Gill RT, Vandamme P, Ussery DW.

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