Plasmo2D

 

Introduction: An ancillary proteomic tool to aid identification of proteins from Plasmodium falciparum. Bioinformatics tools to aid gene and protein sequence analysis have become an integral part of biology in the post-genomic era. Release of the Plasmodium falciparum genome sequence has allowed biologists to define the gene and the predicted protein content as well as their sequences in the parasite. Using pI and molecular weight as characteristics unique to each protein, we have developed a bioinformatics tool to aid identification of proteins from Plasmodium falciparum. The tool makes use of a Virtual 2-DE generated by plotting all the proteins from Plasmodium database on a pI versus molecular weight scale. Proteins are identified by comparing the position of migration of desired protein spots from an experimental 2-DE and that on a virtual 2-DE. The procedure has been automated in the form of user-friendly software called “Plasmo2D”.

Download: Please click here to download the software in the zip compressed format. The program is written in Visual Basic and works on the Windows Operating System. To install the program, unzip the Plasmo2D.zip file and then run the setup.exe file. This will installs the program. If any error occurs while installation, please ignore it.

Help: The pictorial description of the tool and its usage.

 

Complete view of the tool

 

The following notes will be useful while performing the experiment and scanning the 2-DE images for using Plasmo2D software.

 

1)Resolve the total proteins in the cell extract by iso-electric focusing in the first dimension and perform the second dimension SDS-PAGE on a 10% resolving gel.

2)Scan the gel in such a way that the acidic end of the 2-DE gel is to the left side of the image.  Mark 7 cm from the acidic end horizontally and save it as *.jpg or *.gif format.

3)Crop the image of the resolving gel with width 7 cm from the acidic end as marked earlier.  The image would be of dimension 7 cm x height of the resolving gel (cm) on a real scale and save again.

4)Load the image on the software and align the markers of the gel with markers of the software. Tools to move, resize, zoom in, zoom out the gel are provided to help in better alignment.

 

5) When the user clicks on the spot of interest, the red circle will automatically encircle the spot. "Refine cursor location" option can be used to fine tune the position of the red circle.

 

6) The drop down combo box also provides the option to input the stage of the lifecycle in which the experiment is performed. This would help in score analysis.

 

7) "Generate protein report" button would perform the analysis and generate the output window. PlasmoDB protein id, name of the protein, its pI and molecular weight and score is displayed in the output window. A PlasmoDB link is also provided on clicking on the protein of interest in the output window. 

 

8) The user can also "genetare classification report" to find further details about the location and function of the protiens.When user click on the name of the protein, he get the information on it from www.plasmodb.org

                       for support and feedback contact:syama@biochem.iisc.ernet.in or ranjit58@gmail.com