RNA2DSearch is an open source bioinformatics pipeline for searching for RNA secondary structures involved in RNA localization on a genomic scale.

Version 2 is a major revision of the RNA2DSearch method and is currently being developed

Version 1 of the method was recently published in:
Hamilton, R.S., Hartswood, E., Jones, C., Vendra, G., Van De Bor, V., Finnegan, D., & Davis, I. (2008) A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons. RNA, 15, 200-207. [DOI]

Contact:
darogan -at- gmail.com for further details.
(replace -at- with @)

Links:
Davis Lab
Finnegan Lab

RNA2DSearch Version 1

Hamilton, R.S., Hartswood, E., Jones, C., Vendra, G., Van De Bor, V., Finnegan, D., & Davis, I. (2008) A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons. RNA, 15, 200-207. [DOI]

Supplementary Information:

RNA2DSearch Hits Table [txt 15Kb]
RNA2DSearch Full Results Table [txt 6.1Mb]
Flybase Transposable Elements Database [Release 5.1] [Release 5.12 (Lastest Oct08)]
RNA2DSearch RNAMotif description files [G2andIwScore.rnamotif.desc] [GandI.rnamotif.desc] [GandIwScore.rnamotif.desc] [GandIwScoreUU_CAA.rnamotif.desc] [GandIwScoreUU.rnamotif.desc] [GonlyFixed.rnamotif.desc] [IandG2loose.rnamotif.desc] [IandG2mid.rnamotif.desc] [IandG2tight.rnamotif.desc] [IonlyFixed.rnamotif.desc] [JockeyandIwScore.rnamotif.desc]

Source Code:

The code for RNA2DSearch isn't a typical "stand-alone" program, rather a suite of tools made available for researchers to modify and make use of. The code is currently still under development, and is not well commented. As the code progresses, more commenting will be added, working towards a final release of the code as a stand-alone package.

RNA2DSearch Project hosted at GitHub

Prerequisites:

Programming Related:
  • Perl (Modules DBI, LWP::Simple, CGI)
  • MySQL
  • Apache

  • 3rd Party RNA Programs:
  • RNAMotif
  • RNAVienna (RNALfold, RNAfold, RNAdistance, RNAforrester)
  • Mfold (UNAfold)

  • GNU Licence Details:

    This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
    This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details (See http://www.opensource.org/licenses/gpl-license.php).

    Caveats:

    RNA2DSearch works with a MySQL database to store and mine the data produced. However the software below currently does not contain a script to set up the MySQL with the appropriate tables. This script will be included in the final release of the software.

    Russell S. Hamilton Contact: Russell Hamilton: darogan -at- gmail.com