Rtools – Secondary Structural analyses on single RNA sequence

Rtools

:: DESCRIPTION

Rtools is a web server for various secondary structural analyses on single RNA sequences, which provides users with rich information of single RNA sequences using 8 tools.

::DEVELOPER

Rtools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Rtools: a web server for various secondary structural analyses on single RNA sequences.
Hamada M, Ono Y, Kiryu H, Sato K, Kato Y, Fukunaga T, Mori R, Asai K.
Nucleic Acids Res. 2016 Jul 8;44(W1):W302-7. doi: 10.1093/nar/gkw337.

lara 1.3.2a – Sequence-structure Alignment of RNA Sequences

lara 1.3.2a

:: DESCRIPTION

lara (“lagrangian relaxed structural alignment”) is a tool for the sequence-structure alignment of RNA sequences.

::DEVELOPER

Life Sciences Group, Centrum Wiskunde & Informatica

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • T-Coffee

:: DOWNLOAD

 lara

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Jul 27;8:271.
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
Bauer M1, Klau GW, Reinert K.

RNAConSLOpt 1.2 – Predicting Consensus stable local optimal Structures for Aligned RNA Sequences

RNAConSLOpt 1.2

:: DESCRIPTION

RNAConSLOpt is a program for predicting consensus stable local optimal structures (represented by stack configurations) for aligned RNA sequences. RNAConSLOpt can be used to predict consensus alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAConSLOpt

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):498-518. doi: 10.1504/IJBRA.2014.062997.
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Li Y, Zhong C, Zhang S.

RNAscf 1.1 – Consensus Folding of Unaligned RNA sequences

RNAscf 1.1

:: DESCRIPTION

RNAscf is a program for RNA consensus folding for a set of unaligned RNA sequences.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAscf

:: MORE INFORMATION

Citation

J Comput Biol. 2006 Mar;13(2):283-95.
Consensus folding of unaligned RNA sequences revisited.
Bafna V, Tang H, Zhang S.

PAL 1.31 – Pseudoknot Aligment for RNA Sequences

PAL 1.31

:: DESCRIPTION

PAL is an implementation of an efficient algorithm to compute an optimal structural alignment of an RNA sequence against a genomic substring.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PAL

:: MORE INFORMATION

Citation

J Comput Biol. 2008 Jun;15(5):489-504. doi: 10.1089/cmb.2007.0214.
Structural alignment of pseudoknotted RNA.
Han B, Dost B, Bafna V, Zhang S.

iRNAD – Identifying D Modification Sites in RNA sequence

iRNAD

:: DESCRIPTION

iRNAD is a system for identifying whether a RNA sequence contains D modification sites based on machine learning method.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iRNAD: a computational tool for identifying D modification sites in RNA sequence.
Xu ZC, Feng PM, Yang H, Qiu WR, Chen W, Lin H.
Bioinformatics. 2019 May 11. pii: btz358. doi: 10.1093/bioinformatics/btz358.

RNApin – Prediction of Protein Interacting Nucleotides in a RNA Sequence

RNApin

:: DESCRIPTION

RNApin is a Support Vector Machines (SVMs) based web-server for the prediction of Protein Interacting Nucleotides (PINs) in RNA sequences.

::DEVELOPER

RNApin team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.
Panwar B, Raghava GP.
Genomics. 2015 Apr;105(4):197-203. doi: 10.1016/j.ygeno.2015.01.005

RNAcompete / RNAcompete-S – Analysis of RNA Sequence/structure preferences for RNA binding proteins

RNAcompete / RNAcompete-S

:: DESCRIPTION

RNAcompete is a method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts.

RNAcompete-S couples a single-step competitive binding reaction with an excess of random RNA 40-mers to a custom computational pipeline for interrogation of the bound RNA sequences and derivation of SSMs (Sequence and Structure Models).

rnascan is a (mostly) Python suite to scan RNA sequences and secondary structures with sequence and secondary structure PFMs. Secondary structure is represented as weights in different secondary structure contexts, similar to how a PFM represents weights of different nucleotides or amino acids.

::DEVELOPER

Morris Lab , Hughes lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python

:: DOWNLOAD

RNAcompete , RNAcompete-S , rnascan

:: MORE INFORMATION

Citation:

Nat Biotechnol. 2009 Jul;27(7):667-70. doi: 10.1038/nbt.1550. Epub 2009 Jun 28.
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.
Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR.

Cook, K.B., Vembu, S., Ha, K.C.H., Zheng, H., Laverty, K.U., Hughes, T.R., Ray, D., Morris, Q.D., 2017.
RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.
Methods 126, 18–28.

DAFS 0.0.3 – Simultaneous Aligning and Folding of RNA Sequences by Dual Decomposition

DAFS 0.0.3

:: DESCRIPTION

DAFS is a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DAFS

:: MORE INFORMATION

Citation:

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.
Sato K, Kato Y, Akutsu T, Asai K, Sakakibara Y.
Bioinformatics. 2012 Dec 15;28(24):3218-24. doi: 10.1093/bioinformatics/bts612.

CentroidFold 0.0.16 – Predict RNA Secondary Structure from RNA Sequence

CentroidFold 0.0.16

:: DESCRIPTION

CentroidFold predicts an RNA secondary structure from an RNA sequence. FASTA and one-sequence-in-a-line format are accepted for predicting a secondary structure per sequence. It also predicts a consensus secondary structure when a multiple alignment (CLUSTALW format) is given. CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. See the original paper for the details of the algorithm.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CentroidFold

:: MORE INFORMATION

Citation:

Kengo Sato, Michiaki Hamda, Kiyoshi Asai, Toutai Mituyama,
CentroidFold: a web application for RNA secondary structure prediction,
Nucl. Acids Res. (2009) 37 (suppl 2): W277-W280