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Items: 1 to 20 of 138

1.

A structure-based flexible search method for motifs in RNA.

Veksler-Lublinsky I, Ziv-Ukelson M, Barash D, Kedem K.

J Comput Biol. 2007 Sep;14(7):908-26.

PMID:
17803370
2.

RNAMotif, an RNA secondary structure definition and search algorithm.

Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R.

Nucleic Acids Res. 2001 Nov 15;29(22):4724-35.

3.

Identification of consensus RNA secondary structures using suffix arrays.

Anwar M, Nguyen T, Turcotte M.

BMC Bioinformatics. 2006 May 5;7:244.

4.

Structator: fast index-based search for RNA sequence-structure patterns.

Meyer F, Kurtz S, Backofen R, Will S, Beckstette M.

BMC Bioinformatics. 2011 May 27;12:214. doi: 10.1186/1471-2105-12-214.

5.

StemSearch: RNA search tool based on stem identification and indexing.

Milo N, Yogev S, Ziv-Ukelson M.

Methods. 2014 Oct 1;69(3):326-34. doi: 10.1016/j.ymeth.2014.06.002. Epub 2014 Jul 5.

6.
7.

A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences.

Ji Y, Xu X, Stormo GD.

Bioinformatics. 2004 Jul 10;20(10):1591-602. Epub 2004 Feb 12.

PMID:
14962926
8.

RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences.

Pavesi G, Mauri G, Stefani M, Pesole G.

Nucleic Acids Res. 2004 Jun 15;32(10):3258-69. Print 2004.

9.

IncMD: incremental trie-based structural motif discovery algorithm.

Badr G, Al-Turaiki I, Turcotte M, Mathkour H.

J Bioinform Comput Biol. 2014 Oct;12(5):1450027. doi: 10.1142/S0219720014500279.

PMID:
25362841
10.

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures.

Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB.

J Math Biol. 2008 Jan;56(1-2):215-52. Epub 2007 Aug 11.

11.

STR2: a structure to string approach for locating G-box riboswitch shapes in pre-selected genes.

Bergig O, Barash D, Nudler E, Kedem K.

In Silico Biol. 2004;4(4):593-604.

PMID:
15752075
12.

An algorithm for detecting homologues of known structured RNAs in genomes.

Le SY, Maizel JV Jr, Zhang K.

Proc IEEE Comput Syst Bioinform Conf. 2004:300-10.

PMID:
16448023
13.

Discovery of RNA structural elements using evolutionary computation.

Fogel GB, Porto VW, Weekes DG, Fogel DB, Griffey RH, McNeil JA, Lesnik E, Ecker DJ, Sampath R.

Nucleic Acids Res. 2002 Dec 1;30(23):5310-7.

14.

De novo secondary structure motif discovery using RNAProfile.

Zambelli F, Pavesi G.

Methods Mol Biol. 2015;1269:49-62. doi: 10.1007/978-1-4939-2291-8_4.

PMID:
25577372
15.

CMfinder--a covariance model based RNA motif finding algorithm.

Yao Z, Weinberg Z, Ruzzo WL.

Bioinformatics. 2006 Feb 15;22(4):445-52. Epub 2005 Dec 15.

PMID:
16357030
16.

A quantitative analysis of secondary RNA structure using domination based parameters on trees.

Haynes T, Knisley D, Seier E, Zou Y.

BMC Bioinformatics. 2006 Mar 3;7:108.

17.

RNA motif search with data-driven element ordering.

Rampášek L, Jimenez RM, Lupták A, Vinař T, Brejová B.

BMC Bioinformatics. 2016 May 18;17(1):216. doi: 10.1186/s12859-016-1074-x.

18.

ProbKnot: fast prediction of RNA secondary structure including pseudoknots.

Bellaousov S, Mathews DH.

RNA. 2010 Oct;16(10):1870-80. doi: 10.1261/rna.2125310. Epub 2010 Aug 10.

19.

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.

Chen X, He SM, Bu D, Zhang F, Wang Z, Chen R, Gao W.

Bioinformatics. 2008 Sep 15;24(18):1994-2001. doi: 10.1093/bioinformatics/btn327. Epub 2008 Jun 27.

PMID:
18586700
20.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.

Drory Retwitzer M, Polishchuk M, Churkin E, Kifer I, Yakhini Z, Barash D.

Nucleic Acids Res. 2015 Jul 1;43(W1):W507-12. doi: 10.1093/nar/gkv435. Epub 2015 May 4.

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