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Items: 1 to 20 of 119

1.

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, Gaspin C.

RNA. 2011 Nov;17(11):1947-56. doi: 10.1261/rna.2844911. Epub 2011 Sep 23.

2.

Software.ncrna.org: web servers for analyses of RNA sequences.

Asai K, Kiryu H, Hamada M, Tabei Y, Sato K, Matsui H, Sakakibara Y, Terai G, Mituyama T.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W75-8. doi: 10.1093/nar/gkn222. Epub 2008 Apr 25.

3.

LeARN: a platform for detecting, clustering and annotating non-coding RNAs.

Noirot C, Gaspin C, Schiex T, Gouzy J.

BMC Bioinformatics. 2008 Jan 14;9:21. doi: 10.1186/1471-2105-9-21.

5.

CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences.

Liu C, Shi L, Zhu Y, Chen H, Zhang J, Lin X, Guan X.

BMC Genomics. 2012 Dec 20;13:715. doi: 10.1186/1471-2164-13-715.

6.

Plant noncoding RNA gene discovery by "single-genome comparative genomics".

Chen CJ, Zhou H, Chen YQ, Qu LH, Gautheret D.

RNA. 2011 Mar;17(3):390-400. doi: 10.1261/rna.2426511. Epub 2011 Jan 10.

7.

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.

Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W112-7. doi: 10.1093/nar/gkr357. Epub 2011 May 27.

8.

Rfam: annotating non-coding RNAs in complete genomes.

Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4.

9.

CENTROIDFOLD: a web server for RNA secondary structure prediction.

Sato K, Hamada M, Asai K, Mituyama T.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W277-80. doi: 10.1093/nar/gkp367. Epub 2009 May 12.

10.

Efficient known ncRNA search including pseudoknots.

Yuan C, Sun Y.

BMC Bioinformatics. 2013;14 Suppl 2:S25. doi: 10.1186/1471-2105-14-S2-S25. Epub 2013 Jan 21.

11.

GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.

Romualdi A, Siddiqui R, Glöckner G, Lehmann R, Sühnel J.

Bioinformatics. 2005 Sep 15;21(18):3669-71. Epub 2005 Aug 2.

PMID:
16076887
12.

DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data.

Yang JH, Qu LH.

Methods Mol Biol. 2012;822:233-48. doi: 10.1007/978-1-61779-427-8_16.

PMID:
22144203
13.
14.

An Ariadne's thread to the identification and annotation of noncoding RNAs in eukaryotes.

Soldà G, Makunin IV, Sezerman OU, Corradin A, Corti G, Guffanti A.

Brief Bioinform. 2009 Sep;10(5):475-89. doi: 10.1093/bib/bbp022. Epub 2009 Apr 21. Review.

PMID:
19383843
15.

Chain-RNA: a comparative ncRNA search tool based on the two-dimensional chain algorithm.

Lei J, Techa-Angkoon P, Sun Y.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar-Apr;10(2):274-85. doi: 10.1109/TCBB.2012.137.

PMID:
23929857
16.

GenColors: annotation and comparative genomics of prokaryotes made easy.

Romualdi A, Felder M, Rose D, Gausmann U, Schilhabel M, Glöckner G, Platzer M, Sühnel J.

Methods Mol Biol. 2007;395:75-96.

PMID:
17993668
17.

Rfam: annotating families of non-coding RNA sequences.

Daub J, Eberhardt RY, Tate JG, Burge SW.

Methods Mol Biol. 2015;1269:349-63. doi: 10.1007/978-1-4939-2291-8_22.

PMID:
25577390
18.

MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, Médigue C.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9.

19.

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K.

Nucleic Acids Res. 2009 Jan;37(Database issue):D89-92. doi: 10.1093/nar/gkn805. Epub 2008 Oct 23.

20.

RNAcentral: an international database of ncRNA sequences.

RNAcentral Consortium..

Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9. doi: 10.1093/nar/gku991. Epub 2014 Oct 28.

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