:: DESCRIPTION
IM-TORNADO is a pipeline for analysis of paired-end 16S rDNA amplicon data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries.
Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, White B, Nelson H, Kocher JP, Chia N.
PLoS One. 2014 Dec 15;9(12):e114804. doi: 10.1371/journal.pone.0114804. eCollection 2014.
:: DESCRIPTION
IPknot provides services for predicting RNA secondary structures including a wide class of pseudoknots. IPknot can also predict the consensus secondary structure when a multiple alignment of RNA sequences is given. IPknot runs fast and predicts the maximum expected accuracy (MEA) structure using integer programming (IP) with threshold cut.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Y. Kato, K. Sato, K. Asai and T. Akutsu,
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming,
Nucleic Acids Res., 40, W29-W34, 2012
K. Sato, Y. Kato, M. Hamada, T. Akutsu and K. Asai,
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming,
Bioinformatics, vol. 27, no. 13, pp. i85-i93, 2011
:: DESCRIPTION
DREAM is a webserver for the identification of mature microRNA editing events using deep sequencing data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data.
Alon S, Erew M, Eisenberg E.
Bioinformatics. 2015 Apr 2. pii: btv187.
:: DESCRIPTION
CONTRAfold is a novel secondary structure prediction method based on conditional log-linear models (CLLMs), a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. By incorporating most of the features found in typical thermodynamic models, CONTRAfold achieves the highest single sequence prediction accuracies to date, outperforming currently available probabilistic and physics-based techniques. Our result thus closes the gap between probabilistic and thermodynamic models, demonstrating that statistical learning procedures provide an effective alternative to empirical measurement of thermodynamic parameters for RNA secondary structure prediction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Do, C.B., Woods,D.A., and Batzoglou, S. (2006)
CONTRAfold: RNA Secondary Structure Prediction without Energy-Based Models.
Bioinformatics, 22(14): e90-e98.
:: DESCRIPTION
RNA-Redesign utilizes fixed-backbone design to optimize the primary sequence of a RNA to match a desired backbone, in analogy to fundamental tools that have driven major advances in protein engineering.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
RNA-Redesign: a web server for fixed-backbone 3D design of RNA.
Yesselman JD, Das R.
Nucleic Acids Res. 2015 May 11. pii: gkv465.
:: DESCRIPTION
R3D-2-MSA enables users to select nucleotides from representative RNA 3D structures and seamlessly access sequence variants from large and diverse sequence alignments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2015 Jun 5. pii: gkv543.
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.
Cannone JJ, Sweeney BA, Petrov AI, Gutell RR, Zirbel CL, Leontis N
:: DESCRIPTION
AffyRNADegradation helps with the assessment and correction of RNA degradation effects in Affymetrix 3′ expression arrays.
::DEVELOPER
Mario Fasold <fasold at izbi.uni-leipzig.de>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jan 1;29(1):129-31. doi: 10.1093/bioinformatics/bts629. Epub 2012 Oct 24.
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.
Fasold M1, Binder H.
:: DESCRIPTION
pulseR is an R package which aims to handle such count data derived from the pulse-chase RNAseq experiments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Uvarovskii A, Dieterich C.
pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments.
Bioinformatics. 2017 Oct 15;33(20):3305-3307. doi: 10.1093/bioinformatics/btx368. PMID: 29028260.
:: DESCRIPTION
FoldNucleus is a server to calculate the folding nucleus for RNA molecules with known 3D structures-including pseudoknots, tRNAs, hairpins, and ribozymes-and for protein molecules with known 3D structures, as long as they are smaller than 200 amino acid residues.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
Bioinformatics. 2015 Jun 22. pii: btv369.
FoldNucleus: Web server for the prediction of RNA and protein folding nuclei from their 3D structures.
Pereyaslavets LB, Sokolovsky IV, Galzitskaya OV.
:: DESCRIPTION
CRISPRTarget predicts the most likely targets of CRISPR RNAs
::DEVELOPER
Dr Chris Brown’s Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation:
RNA Biol. 2013 May;10(5):817-27. doi: 10.4161/rna.24046. Epub 2013 Mar 14.
CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.
Biswas A1, Gagnon JN, Brouns SJ, Fineran PC, Brown CM.