Tag: RNA Sequence

incaRNAfbinv / RNAfbinv 2.0 – Fragment-based design of RNA sequences

incaRNAfbinv / RNAfbinv 2.0

:: DESCRIPTION

incaRNAfbinv is a web server which implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs.

RNAfbinv is a fragment based RNA design tool. It uses a simulated annealing process to optimize a 2D RNA structure.

::DEVELOPER

incaRNAfbinv team

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RNAfbinv

:: MORE INFORMATION

Citation

Retwitzer MD, Reinharz V, Churkin A, Ponty Y, Waldispühl J, Barash D.
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs.
Bioinformatics. 2020 May 1;36(9):2920-2922. doi: 10.1093/bioinformatics/btaa039. PMID: 31971575.

incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Drory Retwitzer M, Reinharz V, Ponty Y, Waldispühl J, Barash D.
Nucleic Acids Res. 2016 Jul 8;44(W1):W308-14. doi: 10.1093/nar/gkw440. Epub 2016 May 16.

Bioinformatics. 2013 Nov 15;29(22):2938-40. doi: 10.1093/bioinformatics/btt494. Epub 2013 Aug 23.
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.
Weinbrand L1, Avihoo A, Barash D.

pydca 1.0 – Direct Coupling analysis software for Protein and RNA sequences

pydca 1.0

:: DESCRIPTION

pydca is Python implementation of direct coupling analysis (DCA) of residue coevolution for protein and RNA sequence families using the mean-field and pseudolikelihood maximization algorithms.

::DEVELOPER

Multiscale Biomolecular Simulation

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Python
  • C++

:: DOWNLOAD

pydca

:: MORE INFORMATION

Citation

Zerihun MB, Pucci F, Peter EK, Schug A.
pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences.
Bioinformatics. 2020 Apr 1;36(7):2264-2265. doi: 10.1093/bioinformatics/btz892. PMID: 31778142.

repRNA – Web Server for Generating Various Modes of RNA Sequences

repRNA

:: DESCRIPTION

repRNA (representations of RNA sequences) is a web server for generating various modes of RNA sequences

::DEVELOPER

Bin Liu’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Genet Genomics. 2015 Jun 18.
repRNA: a web server for generating various feature vectors of RNA sequences.
Liu B1, Liu F, Fang L, Wang X, Chou KC.

HAlign 2.1 – Fast Multiple Similar DNA/RNA Sequence Alignment

HAlign 2.1

:: DESCRIPTION

HAlign is a package of multi-platform Java software tools, which aimed at large scale multiple similar DNA/RNA sequence alignment. HAlign employs center star multiple sequence alignment strategy.

::DEVELOPER

Dr. Quan Zou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • JRE
  • Hadoop

:: DOWNLOAD

 HAlign

:: MORE INFORMATION

Citation

HAlign: Fast Multiple Similar DNA/RNA Sequence Alignment Based on the Centre Star Strategy.
Zou Q, Hu Q, Guo M, Wang G.
Bioinformatics. 2015 Mar 25. pii: btv177.

StatAlign 3.4 – Bayesian Analysis of Protein, DNA and RNA Sequences

StatAlign 3.4

:: DESCRIPTION

StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results.

::DEVELOPER

StatAlign team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Java

 StatAlign

:: MORE INFORMATION

Citation

Aádám Novák, István Miklós, Rune Lyngsø and Jotun Hein
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees
Bioinformatics (2008) 24 (20): 2403-2404.

Arunapuram P, Edvardsson I, Golden M, Anderson JW, Novák A, Sükösd Z, Hein J (2013)
StatAlign 2.0: Combining statistical alignment with RNA secondary structure prediction. 
Bioinformatics,2013 Mar 1;29(5):654-5. doi:10.1093/bioinformatics/btt025.

KAnalyze 2.0.0 – DNA/RNA Sequence K-mer Toolkit

KAnalyze 2.0.0

:: DESCRIPTION

KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers.

::DEVELOPER

Vannberg Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 KAnalyze

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 18.
KAnalyze: A Fast Versatile Pipelined K-mer Toolkit.
Audano P1, Vannberg F.

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

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