miRTarBase 8.0 – microRNA-target Interactions database

miRTarBase 8.0

:: DESCRIPTION

As a database, miRTarBase has accumulated more than fifty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. While containing the largest amount of validated MTIs, the miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.

::DEVELOPER

Integrative System Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Jul 26;12:300. doi: 10.1186/1471-2105-12-300.
miRTar: an integrated system for identifying miRNA-target interactions in human.
Hsu JB, Chiu CM, Hsu SD, Huang WY, Chien CH, Lee TY, Huang HD.

Nucleic Acids Res. 2011 Jan;39(Database issue):D163-9. doi: 10.1093/nar/gkq1107.
miRTarBase: a database curates experimentally validated microRNA-target interactions.
Hsu SD, Lin FM, Wu WY, Liang C, Huang WC, Chan WL, Tsai WT, Chen GZ, Lee CJ, Chiu CM, Chien CH, Wu MC, Huang CY, Tsou AP, Huang HD.

Gardenia – Compare & Align RNA Structures

Gardenia

:: DESCRIPTION

Gardenia is a program that Compares & aligns RNA secondary structures,without pseudoknots. The resulting alignment takes into account both the primary structure and the secondary structure.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Gardenia

:: MORE INFORMATION

Citation

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet
Alignment of RNA structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008

CG-seq – Comparative Genomics-seq

CG-seq

:: DESCRIPTION

CG-seq is a software pipeline to identify noncoding RNAs in a genomic sequence by comparative analysis and multispecies comparison. It takes as input a genomic sequence (called the target sequence) and a set of other sequences coming from a variety of species to be compared against the target sequences.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java
  • perl

:: DOWNLOAD

 CG-seq

:: MORE INFORMATION

 

RNAfamily – Java Viewer for RNA Secondary Structures

RNAfamily

:: DESCRIPTION

RNAfamily is a simple software tools that enables to display all secondary structures of a family of RNA molecules. It uses the linear backbone representation. RNAfamily provides usual graphical features: zooming, scrolling, etc. Colors of the stems correspond to matching stems. It is also possible to display the nucleotides composing a stem or the whole sequence.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

RNAfamily

:: MORE INFORMATION

For questions about RNAfamily or for bug reports, please contact Helene Touzet

Carnac 0.98 – Predict Secondary Structure for a set of Homologous RNA Sequences

Carnac 0.98

:: DESCRIPTION

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Linux / MacOsX
  • C Complier

:: DOWNLOAD

Carnac

:: MORE INFORMATION

Citation

CARNAC: folding families of related RNAs
Touzet H. and Perriquet O.
Nucl. Acids Res. (2004) 32 (suppl 2): W142-W145

Regliss – RNA Energy Landscape and Saturated Structures

Regliss

:: DESCRIPTION

Regliss proposes to study the energy landscape of a given RNA sequence by considering all locally optimal structures.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Comput Biol. 2012 Oct;19(10):1120-33. doi: 10.1089/cmb.2010.0178.
RNA locally optimal secondary structures.
Saffarian A, Giraud M, de Monte A, Touzet H.

Magnolia – Classification of Coding and Noncoding RNAs

Magnolia

:: DESCRIPTION

Magnolia is a program suite to classify RNA sequences as protein-coding or noncoding genes by comparative analysis. It also produces advanced multiple sequence alignment for the data.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences
Arnaud Fontaine, Antoine de Monte, Helene Touzet
Nucleic Acids Research 36(Web-Server-Issue): 14-18 (2008)

DSIR – Designer of Small Interfering RNA

DSIR

:: DESCRIPTION

DSIR is a tool for siRNA (19 or 21 nt) and shRNA target design.

::DEVELOPER

DSIR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(10):e48057. doi: 10.1371/journal.pone.0048057.
DSIR: assessing the design of highly potent siRNA by testing a set of cancer-relevant target genes.
Filhol O, Ciais D, Lajaunie C, Charbonnier P, Foveau N, Vert JP, Vandenbrouck Y.

RNAsnp 1.2 – Identifying local RNA Structures Disrupted by SNPs

RNAsnp 1.2

:: DESCRIPTION

RNAsnp is a software for efficient detection of local RNA secondary structure changes induced by SNPs

::DEVELOPER

Center for non-coding RNA in Technology and Health (RTH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  RNAsnp

:: MORE INFORMATION

Citation:

Hum Mutat. 2013 Apr;34(4):546-56. doi: 10.1002/humu.22273.
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.

SCFG Structural Entropy 20120907 – Calculate RNA Structural Entropies through Stochastic Context Free Grammars

SCFG Structural Entropy 20120907

:: DESCRIPTION

SCFG Structural Entropy is a software to calculate RNA structural entropies through stochastic context free grammars.

::DEVELOPER

Russell Malmberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SCFG Structural Entropy

:: MORE INFORMATION

Citation

J Theor Biol. 2013 Feb 7;318:140-63. doi: 10.1016/j.jtbi.2012.10.023. Epub 2012 Nov 14.
Information-theoretic uncertainty of SCFG-modeled folding space of the non-coding RNA.
Manzourolajdad A1, Wang Y, Shaw TI, Malmberg RL.