PaVESy 20060803 – Pathway Visualization Editing System

PaVESy 20060803

:: DESCRIPTION

 PaVESy allows user-driven, interactive creation and visualization of pathway maps.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 PaVESy

:: MORE INFORMATION

Citation

A. Luedemann, D. Weicht, J. Selbig, J. Kopka (2004)
PaVESy: Pathway Visualization and Editing System.
Bioinformatics 2004 20(16): 2841-2844

Bi-Force v2 – Large-scale Bicluster Editing and its application to Gene Expression data Biclustering

Bi-Force v2

:: DESCRIPTION

Bi-Force is a novel way of modeling the problem as combinatorial optimization problem on graphs: Weighted Bi-Cluster Editing. It is a very flexible model that can handle arbitrary kinds of multi-condition data sets (not limited to gene expression).

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 Bi-Force

:: MORE INFORMATION

Citation

Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering.
Sun P, Speicher NK, Röttger R, Guo J, Baumbach J.
Nucleic Acids Res. 2014 May;42(9):e78. doi: 10.1093/nar/gku201.

SBGN-ED 1.6 – Editing, Translating and Validating of SBGN Maps

SBGN-ED 1.6

:: DESCRIPTION

SBGN-ED is a VANTED Add-on which allows to create and edit all three types of SBGN maps, that is Process Description, Entity Relationship and Activity Flow, to validate these maps according to the SBGN specifications, to translate maps from the KEGG and MetaCrop pathway databases into SBGN, and to export SBGN maps into several file and image formats.
SBGN (Systems Biology Graphical Notation) is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SBGN-ED

:: MORE INFORMATION

Citation

Tobias Czauderna, Christian Klukas and Falk Schreiber
Editing, Validating, and Translating of SBGN Maps
Bioinformatics (2010)doi: 10.1093/bioinformatics/btq40

Staden 2.0.0b11 – DNA Sequence Assembly , Editing and Analysis

Staden 2.0.0b11

:: DESCRIPTION

Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) .

::DEVELOPER

Staden Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

Staden

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jul 15;26(14):1699-703. doi: 10.1093/bioinformatics/btq268. Epub 2010 May 30.
Gap5–editing the billion fragment sequence assembly.
Bonfield JK1, Whitwham A.

Rodger Staden, David P. Judge and James K. Bonfield.
Analysing Sequences Using the Staden Package and EMBOSS.
Introduction to Bioinformatics. A Theoretical and Practical Approach. Eds. Stephen A. Krawetz and David D. Womble. Human Press Inc., Totawa, NJ 07512 (2003)

RED 0.0.3 – RNA Editing sites Detector

RED 0.0.3

:: DESCRIPTION

RED is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.

::DEVELOPER

RED team

:: SCREENSHOTS

RED

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • JRE

:: DOWNLOAD

 RED

:: MORE INFORMATION

Citation

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.
Sun Y, Li X, Wu D, Pan Q, Ji Y, Ren H, Ding K.
PLoS One. 2016 Mar 1;11(3):e0150465. doi: 10.1371/journal.pone.0150465.

DREAM – Detecting RNA Editing Association with MiRNAs

DREAM

:: DESCRIPTION

DREAM is a webserver for the identification of mature microRNA editing events using deep sequencing data

::DEVELOPER

DREAM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data.
Alon S, Erew M, Eisenberg E.
Bioinformatics. 2015 Apr 2. pii: btv187.

KEGGParser 20140324 – Parsing and Editing KEGG Pathway Maps in Matlab

KEGGParser 20140324

:: DESCRIPTION

KEGGParser is a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment.

::DEVELOPER

 Arsen Arakelyan

:: SCREENSHOTS

KEGGParser

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • MatLab

:: DOWNLOAD

 KEGGParser

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):518-9. doi: 10.1093/bioinformatics/bts730. Epub 2013 Jan 3.
KEGGParser: parsing and editing KEGG pathway maps in Matlab.
Arakelyan A, Nersisyan L.

4SALE 1.7 – Synchronous RNA Sequence and Secondary Structure Alignment and Editing

4SALE 1.7

:: DESCRIPTION

4SALE allows a fast sequence and synchronous secondary structure alignment for large data sets and for the first time synchronous manual editing of aligned sequences and their secondary structures. This study describes an algorithm for the synchronous alignment of sequences and their associated secondary structures as well as the main features of 4SALE used for further analyses and editing. 4SALE builds an optimal and unique starting point for every RNA sequence and structure analysis.

::DEVELOPER

Department of BioinformaticsBiocenterUniversity of Würzburg, Germany

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 4SALE

:: MORE INFORMATION

Citation

Seibel PN, Müller T, Dandekar T & M Wolf (2008):
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
BMC Research Notes 2008, 1:91.