RNAHeliCes 2.0.14 – RNA Folding Space Analysis

RNAHeliCes 2.0.14

:: DESCRIPTION

RNAHeliCes is a tool for RNA folding space analysis. It abstracts from structural detail and maps structures using a position-specific abstraction based on helices.

::DEVELOPER

Cyanolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RNAHeliCes

:: MORE INFORMATION

Citation:

RNA. 2012 Dec;18(12):2135-47. doi: 10.1261/rna.033548.112. Epub 2012 Oct 25.
Abstract folding space analysis based on helices.
Huang J1, Backofen R, Voß B.

BioSeq-Analysis 2.0 / BioSeq-BLM 1.0 – Analyzing DNA, RNA, and Protein Sequences based on Biological Language Models

 BioSeq-Analysis 2.0 / BioSeq-BLM 1.0

:: DESCRIPTION

BioSeq-Analysis is an platform for analyzing DNA, RNA, and protein sequences at sequence level and residue level based on machine learning approaches

BioSeq-BLM is a platform for analyzing DNA, RNA, and protein sequences based on biological language models

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

BioSeq-Analysis / BioSeq-BLM

:: MORE INFORMATION

Citation

Liu B, Gao X, Zhang H.
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches.
Nucleic Acids Res. 2019 Nov 18;47(20):e127. doi: 10.1093/nar/gkz740. PMID: 31504851; PMCID: PMC6847461.

Pse-in-One 1.0.6 – Generating various modes of Pseudo Components of DNA, RNA and Protein Sequences

Pse-in-One 1.0.6

:: DESCRIPTION

Pse-in-One is a web server for generating various modes of pseudo components of DNA, RNA and protein sequences

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 Pse-in-One

:: MORE INFORMATION

Citation

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.
Liu B, Liu F, Wang X, Chen J, Fang L, Chou KC.
Nucleic Acids Res. 2015 Jul 1;43(W1):W65-71. doi: 10.1093/nar/gkv458.

RCAS 1.18.0 – RNA Centric Annotation System

RCAS 1.18.0

:: DESCRIPTION

RCAS facilitates biological discovery from target regions located by methods such as Clip-Seq. RCAS automatically provides dynamic annotations for custom input files that contain transcriptomic target regions.

::DEVELOPER

Bioinformatics & Omics Data Science platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

RCAS

:: MORE INFORMATION

Citation

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A.
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Nucleic Acids Res. 2017 Jun 2;45(10):e91. doi: 10.1093/nar/gkx120. PMID: 28334930; PMCID: PMC5449606.

TFold – RNA Secondary Structure Prediction

TFold

:: DESCRIPTION

Tfold is an algorithm for predicting non-coding RNA secondary structures.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Apr;38(7):2453-66. doi: 10.1093/nar/gkp1067. Epub 2010 Jan 4.
Tfold: efficient in silico prediction of non-coding RNA secondary structures.
Engelen S1, Tahi F.

Rclick – Comparison of RNA 3D Structures

Rclick

:: DESCRIPTION

Rclick is capable of superimposing the RNA 3D structures by using the algorithm of clique matching and 3D least squares fitting.

::DEVELOPER

Rclick team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Rclick: A web server for comparison of RNA 3D structures.
Nguyen MN, Verma C.
Bioinformatics. 2014 Nov 12. pii: btu752.

IM-TORNADO 2.0.3.2 – Illinois Mayo Taxonomy Operations for RNA Database Operations

IM-TORNADO 2.0.3.2

:: DESCRIPTION

IM-TORNADO is a pipeline for analysis of paired-end 16S rDNA amplicon data.

::DEVELOPER

IM-TORNADO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IM-TORNADO

:: 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.

IPknot 1.4.1 – RNA Secondary Structure Prediction including Pseudoknots

IPknot 1.4.1

:: 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

Yuki KatoKengo Sato.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 IPknot

:: 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

DREAM – Detecting RNA Editing Association with MiRNAs

DREAM

:: DESCRIPTION

DREAM is a webserver for the identification of mature microRNA editing events using deep sequencing data

::DEVELOPER

DREAM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: 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.

CONTRAfold 2.02 – RNA Secondary Structure Prediction

CONTRAfold 2.02

:: 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.

CONTRAfold Online Version 

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CONTRAfold

:: 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.