GeneViTo – Genome Visualization Tool

GeneViTo

:: DESCRIPTION

GeneViTo (Genome Visualization Tool) is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction.GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. GeneViTo has already been applied to visualize the genomes of two microbial organisms: the bacterion Chlamydia trachomatis and the archaeon Methanococcus jannaschii.

::DEVELOPER

The Biophysics and Bioinformatics Laboratory 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Java

:: DOWNLOAD

 GeneViTo

:: MORE INFORMATION

Citation

Vernikos, G.S., Gkogkas, C.G., Promponas, V. and Hamodrakas, S.J.
GeneViTo: visualizing gene-product functional and structural features in genomic datasets.”
BMC Bioinformatics 2003 4:53

GEPAT – Genome Expression Pathway Analysis Tool

GEPAT

:: DESCRIPTION

GEPAT (Genome Expression Pathway Analysis Tool) is a modular, scalable and professional-grade software integrating analysis and interpretation of microarray gene expression data.

::DEVELOPER

Department of BioinformaticsBiocenterUniversity of Würzburg, Germany

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 GEPAT

:: MORE INFORMATION

Citation

Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context
Markus Weniger , Julia C Engelmann and Jörg Schultz
BMC Bioinformatics 2007, 8:179

SPC Proteomics Tools 060107 – CDROM Image for SPC tools

SPC Proteomics Tools 060107

:: DESCRIPTION

SPC Proteomics Tools corom contains Seattle Proteome Center (SPC) – Proteomics Tools.

::DEVELOPER

Seattle Proteome Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

 SPC Proteomics Tools

:: MORE INFORMATION

this CD image contains an old version of the SPC tools. Please see the TPP wiki page for the most updated information.

CellExplorer 1.0 – 3D C. elegans atlas Building & Application Tools

CellExplorer 1.0

:: DESCRIPTION

CellExplorer is a package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as well. Some other applications include 3D cell/nuclei segmentation, quantification, gene expression analysis, automatic cell naming/annotation, cell targeting, etc.

::DEVELOPER

Peng Lab @ JANELIA of HHMI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

CellExplorer

:: MORE INFORMATION

Citation:

Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, and Eugene Myers,
A 3D digital atlas of C. elegans and its application to single-cell analyses,”
Nature Methods, doi:10.1038/nmeth.1366, 2009.

Primer Prim’er 5.6.0 – PCR Primer Design Tool

Primer Prim’er 5.6.0

:: DESCRIPTION

Primer Prim’er is a PCR primer design tool that completely automates the primer design process.The software generates vector specific PCR primer sets designed to amplify and insert DNA targets into your labs vectors. Primer prim’er is designed to be a powerful tool for structural genomic efforts as well as a teaching tool. Primer prim’er very customizable. Aside from being able to define and employ your own vectors, a variety of settings can be tailored to your needs.

::DEVELOPER

CABM Structural Bioinformatics Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Flash

:: DOWNLOAD

Primer Prim’er

:: MORE INFORMATION

The previously released PERL-CGI version can be found here.

GenomeComp 1.3 – Whole Genome Compare & Visulization Tool

GenomeComp 1.3

:: DESCRIPTION

GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or strains.

It can be easily used to compare, parsing and visualize large genomic sequences, especially closely related genomes such as inter-species or inter-strains. In addition, it can also show other sequence features like repeat sequence distributions in one whole-genome DNA sequence by comparing the genome to itself.

::DEVELOPER

Chinese National Human Genome Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Linux / Solaris / IRIX

:: DOWNLOAD

GenomeComp

:: MORE INFORMATION

Citation

Yang, J., Wang, J.H., Yao, Z.J., Jin, Q., Shen, Y., Chen, R.S., 2003.
GenomeComp: a visualization tool for microbial genome comparison.
J. Microbiol. Meth. 54, 423-426.

MAGIC Tool 2.1 – MicroArray Genome Imaging & Clustering Tool

MAGIC Tool 2.1

:: DESCRIPTION

MAGIC Tool is an integrated microarray data analysis software.

The purpose of MAGIC Tool is to allow the user to begin with DNA microarray tiff files and end with biologically meaningful information. Comparative hybridization data (glass chips) and Affymetrix data are compatible with MAGIC Tool. You can start with tiff files or expression files.

MAGIC Tool allows the user to change parameters for clustering, data quantification etc.

::DEVELOPER

Laurie Heyer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Mac/ Linux/ UNIX
  • Java

:: DOWNLOAD

MAGIC Tool ;  User’s Guide

:: MORE INFORMATION

Free software with open source.

Paper: MAGIC Tool: Integrated microarray data analysis (Bioinformatics, 2005)

MAExplorer 0.96.34.01 – MicroArray Explorer Tool

MAExplorer 0.96.34.01

:: DESCRIPTION

The MAExplorer is a Java-based bioinformatics exploratory data-analysis and data-mining program for analyzing sets of quantitative spotted cDNA or oligonucleotide microarray data . It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. The exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.

With MAExplorer, it is possible to: 1) analyze the expression of individual genes; 2) analyze the expression of gene families and clusters; 3) compare expression patterns and outliers; 4) directly access other genomic databases for genes of interest. Previously quantified array data is copied to your local computer where it is read by MAExplorer and intermediate results as well as the data mining session state may be saved between data mining sessions.

::DEVELOPER

Dr. Peter Lemkin (LECB/NCI-Frederick) with help from Gregory Thornwall (SAIC) and Jai Evans (DECA/CIT, NIH)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Linux
  • MacOsX
  • Java

:: DOWNLOAD

MAExplorer 0.96.34.01 , Manual

:: MORE INFORMATION

MAExplorer is available as Open Source at the SourceForge at http://maexplorer.sourceforge.net/ under the Mozilla Public License 1.1 (MPL 1.1) with an acompanying LEGAL document required by the U.S. Government.

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