Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LocARNA

被引：174

作者：

Smith, Cameron ^{[1
]}

Heyne, Steffen ^{[1
]}

Richter, Andreas S. ^{[1
]}

Will, Sebastian ^{[1
,2
]}

Backofen, Rolf ^{[1
]}

机构：

[1] Univ Freiburg, Bioinformat Grp, D-79110 Freiburg, Germany

[2] MIT, Dept Math, Cambridge, MA 02139 USA

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

关键词：

GENE-EXPRESSION; PREDICTION; SEQUENCES; ALIGNMENT; TARGETS; REGIONS; GENOME;

D O I：

10.1093/nar/gkq316

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools INTARNA, EXPARNA and LOCARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de.

引用

页码：W373 / W377

页数：5

共 30 条

[1] The eukaryotic genome as an RNA machine [J].

Amaral, Paulo P. ;

Dinger, Marcel E. ;

Mercer, Tim R. ;

Mattick, John S. .

SCIENCE, 2008, 319 (5871) :1787-1789

[2] Fast detection of common sequence structure patterns in RNAs [J].

Backofen, Rolf ;

Siebert, Sven .

JOURNAL OF DISCRETE ALGORITHMS, 2007, 5 (02) :212-228

[3] Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization [J].

Bauer, Markus ;

Klau, Gunnar W. ;

Reinert, Knut .

BMC BIOINFORMATICS, 2007, 8 (1)

[4] Local RNA base pairing probabilities in large sequences [J].

Bernhart, SH ;

Hofacker, IL ;

Stadler, PF .

BIOINFORMATICS, 2006, 22 (05) :614-615

[5] RNAalifold: improved consensus structure prediction for RNA alignments [J].

Bernhart, Stephan H. ;

Hofacker, Ivo L. ;

Will, Sebastian ;

Gruber, Andreas R. ;

Stadler, Peter F. .

BMC BIOINFORMATICS, 2008, 9 (1)

[6] The Ribonuclease P Database [J].

Brown, JW .

NUCLEIC ACIDS RESEARCH, 1999, 27 (01) :314-314

[7] IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions [J].

Busch, Anke ;

Richter, Andreas S. ;

Backofen, Rolf .

BIOINFORMATICS, 2008, 24 (24) :2849-2856

[8] Activation of gene expression by small RNA [J].

Froehlich, Kathrin S. ;

Vogel, Joerg .

CURRENT OPINION IN MICROBIOLOGY, 2009, 12 (06) :674-682

[9] Arthropod 7SK RNA [J].

Gruber, Andreas R. ;

Kilgus, Carsten ;

Mosig, Axel ;

Hofacker, Ivo L. ;

Hennig, Wolfgang ;

Stadler, Peter F. .

MOLECULAR BIOLOGY AND EVOLUTION, 2008, 25 (09) :1923-1930

[10] The Vienna RNA Websuite [J].

Gruber, Andreas R. ;

Lorenz, Ronny ;

Bernhart, Stephan H. ;

Neuboeck, Richard ;

Hofacker, Ivo L. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :W70-W74

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