RNAenn – Energy Parameters and novel algorithms for Extended nearest Neighbor Energy Model of RNA

RNAenn

:: DESCRIPTION

RNAenn computes the partition function and minimum free energy secondary structure for RNA with respect to an extended nearest neighbor energy model.

::DEVELOPER

Clote Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAenn

:: MORE INFORMATION

Citation

Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA.
Dotu I, Mechery V, Clote P.
PLoS One. 2014 Feb 21;9(2):e85412. doi: 10.1371/journal.pone.0085412.

RLooM – RNA Loop Modeling

RLooM

:: DESCRIPTION

RLooM is a web application for homology-based modeling of RNA loops utilizing template structures extracted from the PDB. RLooM allows the insertion and replacement of loop structures of a desired sequence into an existing RNA structure. Furthermore, a comprehensive database of loops in RNA structures can be accessed through the web interface.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Modeling RNA loops using sequence homology and geometric constraints.
Schudoma C, May P, Walther D.
Bioinformatics. 2010 Jul 1;26(13):1671-2. Epub 2010 Apr 28.

INFO-RNA 2.2.0 – A Server for Inverse Folding of RNA

INFO-RNA 2.2.0

:: DESCRIPTION

INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure. Here, you can get an example of the settings and the results.

::DEVELOPER

Bioinformatics Group
Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 INFO-RNA

:: MORE INFORMATION

Citation

Anke Busch, Rolf Backofen.
INFO-RNA – A Server for Fast Inverse RNA Folding Satisfying Sequence Constraints.
Nucleic Acid Res, 2007; 35(Web Server Issue):W310-3.

MARNA 100729 – Server for Multiple Alignment of RNAs

MARNA 100729

:: DESCRIPTION

MARNA (Multiple Alignment of RNAs) is a multiple alignment of RNAs taking into consideration both the primary sequence and the secondary structure. It is based on pairwise comparisons using costs of edit operations. The edit operations can be divided into edit operations on arcs and edit operations on bases. Additionally, MARNA predicts a consensus sequence as well as a consensus structure.

::DEVELOPER

Chair for Bioinformatics Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MARNA

:: MORE INFORMATION

Citation

Sven Siebert and Rolf Backofen,
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons“,
Bioinformatics 2005, Volume 21, Issue 16, 3352-3359

RNAsifter 1.0 – RNA Shape Index Filter

RNAsifter 1.0

:: DESCRIPTION

RNAsifter is a non-rigorous filter for the rfam database, that is based on the abstract shape approach. It exploits the familily specific secondary structure, i.e. it computes shapes for the query-sequence and compares them to a precalculated shape-index. The exact matches deliver – hopefully only few – candiate families in which the query-sequence might fold. Membership for the candidate families is checked with the program cmsearch, afterwards.

::DEVELOPER

S. Janssen, J. Reeder and R. Giegerich.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • perl

:: DOWNLOAD

RNAsifter

:: MORE INFORMATION

Citation

S. Janssen, J. Reeder and R. Giegerich.
Shape based indexing for faster search of RNA family databases.
BMC Bioinformatics. 2008 Feb 29;9:131.

GUUGle 1.2 – Fast Exact Matching under RNA Base Pairing Rules

GUUGle 1.2

:: DESCRIPTION

GUUGle is a utility for fast exact matching under RNA base pairing rules.RNA secondary structure analysis often requires searching for potential helices in large sequence data. We present a utility program GUUGle that efficiently locates potential helical regions under RNA base pairing rules, which include Watson-Crick as well as G-U pairs. It accepts a target and a query set of sequences, and determines all exact matches under RNA rules between target and query sequences that exceed a specified length.

::DEVELOPER

GUUGle team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GUUGle

:: MORE INFORMATION

Citation

GUUGle: A utility for fast exact matching under RNA base pairing rules
W. Gerlach, R. Giegerich
in Bioinformatics, 22(6), Pages:762-764, 2006

RNAhybrid 2.1.2 – Find Minimum Free Energy Hybridisation of RNA

RNAhybrid 2.1.2

:: DESCRIPTION

RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA.The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

::DEVELOPER

RNAhybrid team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/ Windows

:: DOWNLOAD

RNAhybrid

:: MORE INFORMATION

Citation

Marc Rehmsmeier , Peter Steffen, Matthias Höchsmann, Robert Giegerich
Fast and effective prediction of microRNA/target duplexes
RNA, 10:1507-1517, 2004.

pKiss 2.2.12 – Folding RNA Secondary Structures

pKiss 2.2.12

:: DESCRIPTION

pKiss is a tool for folding RNA secondary structures, including two limited classes of pseudoknots.

::DEVELOPER

Stefan Janssen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pKiss

:: MORE INFORMATION

Citation

J Comput Biol. 2008 Mar;15(2):139-63. doi: 10.1089/cmb.2007.0198.
Novel and efficient RNA secondary structure prediction using hierarchical folding.
Jabbari H, Condon A, Zhao S.

RNAmmer 1.2 – Ribosomal RNA Sub Units

RNAmmer 1.2

:: DESCRIPTION

RNAmmer  predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

RNAmmer Source Code

:: MORE INFORMATION

Citation

RNAmmer: consistent and rapid annotation of ribosomal RNA genes
Karin Lagesen, Peter Hallin, Einar Andreas Rødland, Hans-Henrik Stærfeldt, Torbjørn Rognes and David W. Ussery
Nucl. Acids Res. (2007) 35 (9): 3100-3108

metaRNAmodules 1.0.2 – Automated RNA 3D Module Extraction and Modeling

metaRNAmodules 1.0.2

:: DESCRIPTION

metaRNAmodules is a pipeline which completely automates extracting putative FR3D modules and mapping of such modules to Rfam alignments to obtain comparative evidence.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  metaRNAmodules

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Dec;41(22):9999-10009. doi: 10.1093/nar/gkt795.
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.