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

xFITOM

:: 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

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

Hautaniemi Lab

:: 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

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 0.0.15 – Predict RNA Secondary Structure from RNA Sequence

CentroidFold 0.0.15

:: 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

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

JCI BioInfo 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.

CDSfold 0.2 – Designing Protein-coding RNA Sequence

CDSfold 0.2

:: DESCRIPTION

CDSfold is an algorithm for designing a protein-coding sequence with the most stable secondary structure.

::DEVELOPER

CDSfold team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Vienna RNA package

:: DOWNLOAD

 CDSfold

:: MORE INFORMATION

Citation

CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure.
Terai G, Kamegai S, Asai K.
Bioinformatics. 2015 Nov 20. pii: btv678.

FASTR – Format for Concomitant Representation of RNA Sequence and Secondary Structure Information

FASTR

:: DESCRIPTION

FASTR is a novel storage format for concomitant representation of RNA sequence and structure.

::DEVELOPER

Bio-Sciences R&D Division, TCS Innovation Labs

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • RNAfold
  • JRE

:: DOWNLOAD

 FASTR

 

:: MORE INFORMATION

Citation

J Biosci. 2015 Sep;40(3):571-7.
FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.
Bose T1, Dutta A, Mh M, Gandhi H, Mande SS.

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

repRNA team

:: 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.

antaRNA 1.09 – Ant Colony Optimized RNA Sequence Design

antaRNA 1.09

:: DESCRIPTION

antaRNA applies the principle of Ant Colony optimization (ACO) to the problem of inverse folding a RNA structure i.e. finding a suitable sequence, which can fold into that structure.

::DEVELOPER

Bioinformatics Group, Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 antaRNA

:: MORE INFORMATION

Citation

antaRNA – Ant Colony Based RNA Sequence Design.
Robert K, Martin M, Rolf B.
Bioinformatics. 2015 May 27. pii: btv319.

RNAfbinv – Fragment-Based Design of RNA sequences

RNAfbinv

:: DESCRIPTION

RNAfbinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes.

::DEVELOPER

RNAfbinv team

:: SCREENSHOTS

RNAfbinv

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

RNAfbinv

:: MORE INFORMATION

Citation

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.