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.

GEDpm-cg – Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum

GEDpm-cg

:: DESCRIPTION

GEDpm-cg enables users to perform the efficient, automated and high-throughput design of single nucleotide editing in C. glutamicum chromosome. The counter-selection HR system and the overlap-based assembly method were chosen as the loading techniques. Homologous arms and primers required for genetic modification, vector DNA assembly and sequencing verification were provided as design results.

::DEVELOPER

Biodesign Centre, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web server
  • Python

:: DOWNLOAD

GEDpm-cg

:: MORE INFORMATION

Citation

Yang Y, Mao Y, Liu Y, Wang R, Lu H, Li H, Luo J, Wang M, Liao X, Ma H.
GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum.
Front Bioeng Biotechnol. 2021 Oct 15;9:768289. doi: 10.3389/fbioe.2021.768289. PMID: 34722482; PMCID: PMC8554027.

sgRNA online 1.2 – Identifies efficient sgRNAs for CRISPR editing of mouse and human Genomes

sgRNA online 1.2

:: DESCRIPTION

sgRNA online is an online tool that identifies efficient sgRNAs for CRISPR editing of mouse and human genomes. It supports both classic Cas9 and xCa9 3.7.

::DEVELOPER

Yongbing Zhao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 No

:: MORE INFORMATION

 

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.

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

:: 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.

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)

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

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