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Dinucleotide controlled null models for comparative RNA gene prediction.

Gesell T, Washietl S.

BMC Bioinformatics. 2008 May 27;9:248.PMID: 18505553 [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

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

Bradley RK, Pachter L, Holmes I.

Bioinformatics. 2008 Dec 1;24(23):2677-83. Epub 2008 Sep 16.PMID: 18796475 [PubMed - indexed for MEDLINE]Related articlesFree article

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.PMID: 16477324 [PubMed - indexed for MEDLINE]Related articlesFree article

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.

Anandam P, Torarinsson E, Ruzzo WL.

Bioinformatics. 2009 Mar 1;25(5):668-9. Epub 2009 Jan 9.PMID: 19136551 [PubMed - indexed for MEDLINE]Related articles

Fast and reliable prediction of noncoding RNAs.

Washietl S, Hofacker IL, Stadler PF.

Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2454-9. Epub 2005 Jan 21.PMID: 15665081 [PubMed - indexed for MEDLINE]Related articlesFree article

Strategies for measuring evolutionary conservation of RNA secondary structures.

Gruber AR, Bernhart SH, Hofacker IL, Washietl S.

BMC Bioinformatics. 2008 Feb 26;9:122.PMID: 18302738 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering.

Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R.

PLoS Comput Biol. 2007 Apr 13;3(4):e65. Epub 2007 Feb 22.PMID: 17432929 [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

A local multiple alignment method for detection of non-coding RNA sequences.

Tabei Y, Asai K.

Bioinformatics. 2009 Jun 15;25(12):1498-505. Epub 2009 Apr 17.PMID: 19376823 [PubMed - indexed for MEDLINE]Related articles

Accelerated probabilistic inference of RNA structure evolution.

Holmes I.

BMC Bioinformatics. 2005 Mar 24;6:73.PMID: 15790387 [PubMed - indexed for MEDLINE]Related articlesFree article

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.PMID: 15804354 [PubMed - indexed for MEDLINE]Related articlesFree article

Murlet: a practical multiple alignment tool for structural RNA sequences.

Kiryu H, Tabei Y, Kin T, Asai K.

Bioinformatics. 2007 Jul 1;23(13):1588-98. Epub 2007 Apr 25.PMID: 17459961 [PubMed - indexed for MEDLINE]Related articlesFree article

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.

Gruber AR, Neuböck R, Hofacker IL, Washietl S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W335-8. Epub 2007 Apr 22.PMID: 17452347 [PubMed - indexed for MEDLINE]Related articlesFree article

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

Havgaard JH, Torarinsson E, Gorodkin J.

PLoS Comput Biol. 2007 Oct;3(10):1896-908. Epub 2007 Aug 20.PMID: 17937495 [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.

Proc IEEE Comput Syst Bioinform Conf. 2004:290-9.PMID: 16448022 [PubMed - indexed for MEDLINE]Related articles

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

Uzilov AV, Keegan JM, Mathews DH.

BMC Bioinformatics. 2006 Mar 27;7:173.PMID: 16566836 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying structural noncoding RNAs using RNAz.

Washietl S, Hofacker IL.

Curr Protoc Bioinformatics. 2007 Sep;Chapter 12:Unit 12.7.PMID: 18428784 [PubMed - indexed for MEDLINE]Related articles

STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time.

Dalli D, Wilm A, Mainz I, Steger G.

Bioinformatics. 2006 Jul 1;22(13):1593-9. Epub 2006 Apr 13.PMID: 16613908 [PubMed - indexed for MEDLINE]Related articlesFree article

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

Bauer M, Klau GW, Reinert K.

BMC Bioinformatics. 2007 Jul 27;8:271.PMID: 17662141 [PubMed - indexed for MEDLINE]Related articlesFree article