SePIA – RNA Sequence Processing, Integration, and Analysis

SePIA

:: DESCRIPTION

SePIA is a comprehensive RNA Sequencing workflow standardizing Processing, Integration, and Analysis of large-scale sequencing data. It provides a systematic, pipeline architecture to manage, individually analyze, and integrate both small-RNA and RNA data.

::DEVELOPER

Systems Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SePIA

:: MORE INFORMATION

Citation

SePIA: RNA and small RNA sequence processing, integration, and analysis.
Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S.
BioData Min. 2016 May 20;9:20. doi: 10.1186/s13040-016-0099-z

FiToM / xFITOM / jFITOM 201605 – Detection of Binding Sites in DNA or RNA Sequences

FiToM / xFITOM / jFITOM 201605

:: DESCRIPTION

FITOM is a computer program for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user.

xFITOM is a fully featured GUI-enabled version of FITOM for Ms-Windows platforms that integrates additional functionality. The program provides an easy to use graphical user interface (GUI) to define all the relevant options for locating binding sites in genetic sequences.

jFITOM is a Java version of FITOM.

::DEVELOPER

the Erill Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

FITOM , xFITOM , jFITOM

:: MORE INFORMATION

Citation

Erill, I; O’Neill, M.C.
A reexamination of information theory-based methods for DNA-binding site identification
BMC Bioinformatics. 2009 Feb 11;10(1):57

Bhargava, N. & Erill, I. (2010)
xFITOM: a generic GUI tool to search for transcription factor binding sites”,
Bioinformation 5(2) 49-51

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

  NO

:: 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

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.