:: DESCRIPTION
PLEXY is a tool for computation of optimal thermodynamical interactions of a box C/D snoRNA (Small nucleolar RNAs) with a putative target RNA.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Jan 15;27(2):279-80. Epub 2010 Nov 13.
PLEXY: efficient target prediction for box C/D snoRNAs.
Kehr S, Bartschat S, Stadler PF, Tafer H.
:: DESCRIPTION
RNAsnoop is a tool especially designed to search for putative interactions between a H/ACA snoRNA stem and a list of target sequence. RNAsnoop implements a dynamic programming algorithm that computes thermodynamically optimal H/ACA-RNA interactions in an efficient scanning variant. Complemented by an support vector machine (SVM)-based machine learning approach to distinguish true binding sites from spurious solutions and a system to evaluate comparative information, it presents an efficient and reliable tool for the prediction of H/ACA snoRNA target sites. We apply RNAsnoop to identify the snoRNAs that are responsible for several of the remaining ‘orphan’ pseudouridine modifications in human rRNAs, and we assign a target to one of the five orphan H/ACA snoRNAs in Drosophila.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Mar 1;26(5):610-6. Epub 2009 Dec 16.
RNAsnoop: efficient target prediction for H/ACA snoRNAs.
Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF.
:: DESCRIPTION
RNAxs is a tool especially created to design potent siRNAs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Biotechnol. 2008 May;26(5):578-83. Epub 2008 Apr 27.
The impact of target site accessibility on the design of effective siRNAs.
Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL.
:: DESCRIPTION
RNAplex is a tool especially created to rapidly search for short interactions between two long RNAs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2008 Nov 15;24(22):2657-63. Epub 2008 Apr 23.
RNAplex: a fast tool for RNA-RNA interaction search.
Tafer H, Hofacker IL.
:: DESCRIPTION
The Kinwalker algorithm performs cotranscriptional folding of RNAs, starting at a user a specified structure (default: open chain) and ending at the minimum free energy structure. Folding events are performed between transcription of additional bases and are regulated by barrier heights between the source and target structure.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Mol Biol. 2008 May 23;379(1):160-73. Epub 2008 Mar 6.
Folding kinetics of large RNAs.
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C.
:: DESCRIPTION
HelixPSO (Particle Swarm Optimizer) is a multi swarm algorithm that searches the conformation space of an RNA sequence for low lying structures. Fitness is a combination of free energy and agreement with the centroid structure in the thermodynamic ensemble. HelixPSO has been used on sequences of up to 1500 nucleotides.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ConStruct (construction of RNA consensus structures) is an RNA alignment editor and consensus structure prediction tool. It combines multiple sequence alignment, thermodynamic structure prediction and statistics in a semiautomatical fashion. Its sophisticated GUI guides the user through correcting an initial sequence alignment with respect to a consensus structure.
::DEVELOPER
Gerhard Steger <steger@biophys.uni-duesseldorf.de>,Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie, Universitätsstr
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Wilm, A., Linnenbrink, K. & Steger, G. (2008)
ConStruct: improved construction of RNA consensus structures.
BMC Bioinformatics 9, 219.
:: DESCRIPTION
SPF (Structural Pattern Finder) is a tool that identify regions of a given RNA or DNA sequence that possess a high probability of being structured. This is achieved by computing, for each region, the difference between the folding free energy of the native sequence with the average folding free energy of randomized sequences of the same base composition.
::DEVELOPER
Laboratoire de Biologie Informatique et Théorique
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
I. Barrette, G. Poisson, P. Gendron and F. Major (2000)
Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching,
Nucleic Acids Res. 2001 February 1; 29(3): 753–758.
:: DESCRIPTION
The HotKnots program predicts secondary structures of RNA molecules with or without pseudoknots.
::DEVELOPER
BETA LAB – University of British Columbia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Ren, J., Rastegari, B., Condon, A., and Hoos, H. H. (2005).
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
RNA, 11(10), 1494–1504.
:: DESCRIPTION
The AveRNA program predicts secondary structures by combining structures obtained from 11 other prediction programs.
::DEVELOPER
BETA LAB – University of British Columbia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nima Aghaeepour and Holger Hoos:
Ensemble-based Prediction of RNA Secondary Structures.
RNA, submitted for publication, May 2011.
