Carnac 0.98 – Predict Secondary Structure for a set of Homologous RNA Sequences

Carnac 0.98

:: DESCRIPTION

Carnac is a software tool for analysing the hypothetical secondary structure of a family of homologous RNA. It aims at predicting if the sequences actually share a common secondary structure. When this structure exists, Carnac is then able to correctly recover a large amount of the folded stems. The input is a set of single-stranded RNA sequences that need not to be aligned. The folding strategy relies on a thermodynamic model with energy minimization. It combines information coming from locally conserved elements of the primary structure and mutual information between sequences with covariations too.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
C Complier

:: DOWNLOAD

Carnac

:: MORE INFORMATION

Citation

CARNAC: folding families of related RNAs
Touzet H. and Perriquet O.
Nucl. Acids Res. (2004) 32 (suppl 2): W142-W145

Structator 1.1 – Fast Index-based Search for RNA Sequence-structure Patterns

Structator 1.1

:: DESCRIPTION

Structator is a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns.

::DEVELOPER

Structator team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX

:: DOWNLOAD

Structator

:: MORE INFORMATION

Citation

Meyer, F., Kurtz, S., Backofen, R., Will, S., Beckstette, M. (2011).
Structator: fast index-based search for RNA sequence-structure patterns.
BMC Bioinformatics 12:214.

pRNAm-PC – Predicting N6-methyladenosine sites in RNA sequences

pRNAm-PC

:: DESCRIPTION

The web-server pRNAm-PC is used to predict the dentify the N⁶-methyladenosine (m⁶A).

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

pRNAm-PC: Predicting N6-methyladenosine sites in RNA sequences via physical-chemical properties.
Liu Z, Xiao X, Yu DJ, Jia J, Qiu WR, Chou KC.
Anal Biochem. 2015 Dec 31;497:60-67. doi: 10.1016/j.ab.2015.12.017.

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

:: 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

:: 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

:: 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