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Results: 1 to 20 of 107

1.

Shape based indexing for faster search of RNA family databases.

Janssen S, Reeder J, Giegerich R.

BMC Bioinformatics. 2008 Feb 29;9:131. doi: 10.1186/1471-2105-9-131.

PMID:
18312625
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Query-dependent banding (QDB) for faster RNA similarity searches.

Nawrocki EP, Eddy SR.

PLoS Comput Biol. 2007 Mar 30;3(3):e56. Epub 2007 Feb 7.

PMID:
17397253
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

FastR: fast database search tool for non-coding RNA.

Bafna V, Zhang S.

Proc IEEE Comput Syst Bioinform Conf. 2004:52-61.

PMID:
16447999
[PubMed - indexed for MEDLINE]
4.

Annotating non-coding RNAs with Rfam.

Griffiths-Jones S.

Curr Protoc Bioinformatics. 2005 Apr;Chapter 12:Unit 12.5. doi: 10.1002/0471250953.bi1205s9.

PMID:
18428745
[PubMed - indexed for MEDLINE]
5.

Locomotif: from graphical motif description to RNA motif search.

Reeder J, Reeder J, Giegerich R.

Bioinformatics. 2007 Jul 1;23(13):i392-400.

PMID:
17646322
[PubMed - indexed for MEDLINE]
Free Article
6.

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.

PMID:
21619640
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy.

Weinberg Z, Ruzzo WL.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i334-41.

PMID:
15262817
[PubMed - indexed for MEDLINE]
Free Article
8.

Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns.

Meyer F, Kurtz S, Beckstette M.

BMC Bioinformatics. 2013 Jul 17;14:226. doi: 10.1186/1471-2105-14-226.

PMID:
23865810
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.

Tabei Y, Tsuda K, Kin T, Asai K.

Bioinformatics. 2006 Jul 15;22(14):1723-9. Epub 2006 May 11.

PMID:
16690634
[PubMed - indexed for MEDLINE]
Free Article
10.

Mining frequent stem patterns from unaligned RNA sequences.

Hamada M, Tsuda K, Kudo T, Kin T, Asai K.

Bioinformatics. 2006 Oct 15;22(20):2480-7. Epub 2006 Aug 14.

PMID:
16908501
[PubMed - indexed for MEDLINE]
Free Article
11.

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities.

Roshan U, Chikkagoudar S, Livesay DR.

BMC Bioinformatics. 2008 Jan 28;9:61. doi: 10.1186/1471-2105-9-61.

PMID:
18226231
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.

Alekseyenko AV, Lee CJ.

Bioinformatics. 2007 Jun 1;23(11):1386-93. Epub 2007 Jan 18.

PMID:
17234640
[PubMed - indexed for MEDLINE]
Free Article
13.

Data mining of imperfect double-stranded RNA in 3' untranslated regions of eukaryotic mRNAs.

Le SY, Maizel JV Jr.

Biomol Eng. 2007 Sep;24(3):351-9. Epub 2007 Mar 3.

PMID:
17482872
[PubMed - indexed for MEDLINE]
14.

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.

Hertel J, Stadler PF.

Bioinformatics. 2006 Jul 15;22(14):e197-202.

PMID:
16873472
[PubMed - indexed for MEDLINE]
Free Article
15.

RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure.

Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X.

BMC Bioinformatics. 2008 Mar 31;9:176. doi: 10.1186/1471-2105-9-176.

PMID:
18373878
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Designing secondary structure profiles for fast ncRNA identification.

Sun Y, Buhler J.

Comput Syst Bioinformatics Conf. 2008;7:145-56.

PMID:
19642276
[PubMed - indexed for MEDLINE]
Free Article
17.

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]
Free PMC Article
18.

Identification of consensus RNA secondary structures using suffix arrays.

Anwar M, Nguyen T, Turcotte M.

BMC Bioinformatics. 2006 May 5;7:244.

PMID:
16677380
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An algorithm for searching RNA motifs in genomic sequences.

Liu J, Ma B, Zhang K.

Biomol Eng. 2007 Sep;24(3):343-50. Epub 2007 Mar 3.

PMID:
17482512
[PubMed - indexed for MEDLINE]
20.

Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements.

Doh ST, Zhang Y, Temple MH, Cai L.

BMC Bioinformatics. 2007 Mar 15;8:94.

PMID:
17362514
[PubMed - indexed for MEDLINE]
Free PMC Article

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