• Rating:
  • Version: 1.0.0
  • Publisher:
  • File Size: 1.1 KB
  • Date: Aug 31, 2010
  • License: Freeware
  • Category:
    Graphing Software
MaGnET Download
Free Download MaGnET 1.0.0

MaGnET is a Malaria Genome Exploration Tool. View malaria parasite datasets with this tool. MaGnET is a software tool for visualisation and exploration of large-scale datasets relating to the malaria parasite. At present the program is focused on Plasmodium falciparum, as this was the first Plasmodium species to have its genome sequenced and is the focus of several genomic-scale gene characterisation studies.

The program allows users to examine features of groups of genes across different datasets. It offers alternative views of the data, for example, while in the whole genome view, you may select a gene expression dataset to display against the genomic location of the genes.

If you click on a chromosome it will open in a chromosome viewing window allowing you to examine the genes more closely. The protein-protein interaction viewer allows you to navigate the interaction network for genes of interest. Overlaying messenger RNA and protein expression data onto the interactome is a useful feature.

Another section allows you to query the database and retrieve results in the form of a table. The expression data viewer currently offers the capability to view the gene expression profile of individual genes and to compare the profiles of small groups of genes. In addition, a whole-genome expression viewer is planned and will hopefully be available soon. In all cases, it is possible to open a fact sheet listing detailed genomic and functional information about a particular gene.

The fact sheet also provides the protein and and nucleotide sequences, ortholog and paralog data, list of known interactions, Gene Ontology and InterPro annotation, links to protein structures (solved and modelled) and linkouts to other online resources.

MaGnET is available to use online as a Java applet. Alternatively, you can use Java Web Start to download the application and run it from your desktop.

To view the genomic location of the selected genes in group A:

1. In the light blue 'Genome' panel, select 'P. falciparum 3D7 genome' and click 'Launch viewer'. The genome viewer should open displaying the 14 nuclear chromosomes, the mitochondrial and the plastid (apicoplast) chromosomes. The location of the genes in group A are highlighted as orange lines. Lines on the right side of the chromosome are genes on the forward (w) strand and lines on the left side are on the reverse (c) strand.
2. Find the location of the gene PF10_0213 by typing it's identifier into the search bar at the top of window, and pressing 'Find'. It will now be highlighted in purple.
3. To view chromosome 10 in closer detail, double click on it.
4. Scroll along the chromosome until reaching the purple-highlighted gene PF10_0213. Click on the 'Clear' button at the top of the window. PF10_0213 should revert to orange.
5. Under the 'Genes' menu, click 'Introns'.
6. To display introns the scale must be equal to or less than 50 bp/pixel. Zoom in to 30 bp/pixel by pressing the 'Zoom in' button. The introns are displayed as pink regions within a gene.
To view the gene's product name:
7. Click once on the gene PF10_0213. Its product name should appear at the top of the panel.
To find out more about a particular gene, view its factsheet:
8. Double click on gene PF10_0213.

Please Note: this program is a Java Web Start Application, you need to right-click on the download file and choose "Launch".

* Java
* Internet Connection

The license of this software is Freeware, you can free download and free use this graphing software.

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