Tag: Non-protein-coding RNA

ApolloRNA 1.11.8 – Apollo for non Protein Coding RNA (ncRNA) Identification

ApolloRNA 1.11.8

:: DESCRIPTION

ApolloRNA is an extension for ncRNA identification of the Apollo environment , a genome annotation viewer and editor.

::DEVELOPER

the Biometry and Artificial Intelligence Laboratory of INRA Toulouse, France

:: SCREENSHOTS

ApolloRNA

:: REQUIREMENTS

:: DOWNLOAD

 ApolloRNA

:: MORE INFORMATION

Citation:

Cros MJ, Moisan A, Cierco-Ayrolles C, Gaspin C.
Visualizing and exploring genomic information for non-protein-coding RNA identification using ApolloRNA.
Nature Protocols. (2007) doi: 10.1036/nprot.20.07.285.

RNAspace 1.2 – Platform for Non-protein-coding RNA Annotation

RNAspace 1.2

:: DESCRIPTION

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation. The platform allows running in an integrated environment a variety of ncRNA gene finders, to explore results with dedicated tools for comparison, visualization and edition of putative ncRNAs and to export them in various formats

::DEVELOPER

RNAspace Team

:: SCREENSHOTS

Document3

:: REQUIREMENTS

  • Linux
  • Python
  • cherrypy
  • cheetah
  • blastall, bl2seq
  • clustalw
  • Vienna RNA package
  • Perl

:: DOWNLOAD

 RNAspace

:: MORE INFORMATION

Citation

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

Darn 1.0 – Non-protein-coding RNA Detection

Darn 1.0

:: DESCRIPTION

Darn is a RNA motif search tool. It finds all the subsequences that match a specified motif on some input genomic sequence(s).Darn uses a weighted constraint solver to localize the portions of a genomic sequence that match a motif. The motif is expressed in a specific language (see section 5). Some motif descriptors are provided with the software for FMN, Lysine, RNaseP, SAM,snoRNA C/D-box and tRNA search.

::DEVELOPER

Matthias Zytnicki 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Darn

:: MORE INFORMATION

Citation

M. Zytnicki, C. Gaspin, T. Schiex.
Darn – A Weighted Constraint Solver for RNA Motif Localization.
Constraints, Volume 13 (2008).