Locomotif – Visual Design of RNA Motifs

Locomotif

:: DESCRIPTION

Locomotif is a GUI-based program that allows for the visual design of RNA motifs. The graphical structures are then translated into executable programs to be used for searching a motif in a sequence (plain text or FASTA format).

::DEVELOPER

Janina Reeder

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

Locomotif

:: MORE INFORMATION

Citation

Reeder, Janina, Reeder, Jens and Giegerich, Robert
Locomotif: From Graphical Motif Description to RNA Motif Search
Bioinformatics, 23(13) , Pages:i392-400, 2007

RMfam 0.3 – Multiple Alignments and Probabilistic Models of RNA Motifs

RMfam 0.3

:: DESCRIPTION

RMfam is a database of annotated multiple sequence alignments and probabilistic models for a number of RNA motifs.

::DEVELOPER

Paul Gardner

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 RMfam

:: MORE INFORMATION

Citation

Annotating RNA motifs in sequences and alignments.
Gardner PP, Eldai H.
Nucleic Acids Res. 2015 Jan;43(2):691-8. doi: 10.1093/nar/gku1327

CMfinder 2.0 – Predict RNA Motifs in Unaligned Sequences

CMfinder 2.0

:: DESCRIPTION

CMfinder is a tool to predict RNA motifs in unaligned sequences. It is an expectation maximization algorithm using covariance models for motif description, featuring novel integration of multiple techniques for effective search of motif space, and a Bayesian framework that blends mutual information-based and folding energy-based approaches to predict structure in a principled way.

::DEVELOPER

Zizhen Yao, Zasha Weinberg, Walter L. Ruzzo , The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

CMfinder ; Manual

:: MORE INFORMATION

Citation

Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15.
De novo discovery of structured ncRNA motifs in genomic sequences.
Ruzzo WL, Gorodkin J.

Z. Yao, Z. Weinberg, W. Ruzzo, “CMfinder–a covariance model based RNA motif finding algorithm”, Bioinformatics, vol. 22 (2006) 445-52. Pubmed 16357030.

RegRNA 2.0 – an integrated web server for Identifying Functional RNA Motifs and Sites

RegRNA 2.0

:: DESCRIPTION

RegRNA is an integrated web server to comprehensively identify homologs of functional RNA motifs and sites in an RNA sequence.

::DEVELOPER

Molecular Bioinformatics Center,  National Chiao Tung University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Chang TH, Huang HY, Hsu JB, Weng SL, Horng JT, Huang HD:
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs.
BMC bioinformatics 2013, 14 Suppl 2:S4

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements.
Huang HY, Chien CH, Jen KH, Huang HD.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W429-34.