Other tools for exploring genomic data sets

Protannot Beta - A tool for visualizing the effects of alternative splicing on protein sequence and function

This program from the Loraine Lab at the University of North Carolina at Charlotte implements many useful features designed for understanding how alternative splicing, alternative promoters, and alternative polyadenylation can affect the sequence and function of proteins encoded by diverse variants expressed from the same gene. If you have questions or suggestions about the software, we would love to hear them.

For suggestions, bug reports, and comments, please contact Hiral Vora (hvora1uncc.edu) who is the lead programmer on the project.

To download and launch ProtAnnot, click the button below:

Start Protannot with Java Web Start

TableView - Interactive scatter plots and other views on tabular data

This program by Jim Johnson of the University of Minnesota implements many useful features that are well-suited for visualization of genomic data. One of our favorites includes an interactive spreadsheet/scatter plot view that is particularly useful for viewing expression data from multiple experiments.

TableView can present data in spreadsheet format, which lets you sort, copy and paste rows, etc. It also lets you view scatter plots comparing columns in the spreadsheet. And when you select points in the scatter plot, the spreadsheet responds by highlighting the corresponding rows. We started using TableView because of this feature, but it can do a lot more.

So far as we know, there is no University of Minnesota download site for the program; the group that released it disbanded in 2008. However, the author of the program has kindly provided a version which you are welcome to download here. If you like the program and find it useful, please let us know.

To download and launch TableView, click the button below:

Start TableView with Java Web Start

If you would like more information about TableView, we recommend you read this Applications Note that appeared in the journal Bioinformatics.