Best Platform For Making Dot Plot
Entering edit mode
10.6 years ago

I have to make a Dot plot program (specific Dot-plot of bioinformatic) in which two complete genome of eukaryotes can be aligned. The GUI of that dot-plot should be rich enough that after alignment specific region on dot plot can be selected ( regions like palindromic line, minisatellites, conserved regions etc) and sequence of these regions can also be retrieved.

Basically I have been using .NET platform (more specifically using C#), for 3 years as a graduate student, for developing any web and desktop application but at this point I am thinking Python or Java would be more beneficial for doing this project because alot of work had been done regarding Bioinformatics like BioPython and BioJava libraries.

So my question is that what platform would be helpful for me to complete this project?

python java • 13k views
Entering edit mode
10.6 years ago
Josh Herr 5.7k

You can design platform to do dot plots in either Python or Java, but why invent the wheel when others have already done what you are asking (at least you could use other aligners as a jumping off point for your own dot plot aligner)?

There are numerous tools that will give you a dot plot of two sequences. I am going to plug a program from my colleague at Penn State, Bob Harris, called LASTZ. It's come in handy for me when I have made dot plots in the past. There are many output files formats in the documentation, including a R output for easy graphing in R. There's no GUI, so you'll have to use it at the command line. If you require a GUI, there are some handy dotplot functions in GALAXY; go to tools enter "dotplot" and it will give you a few options depending on the details of your sequence comparison.

Entering edit mode

You are right at this point because I have not explain all my work. Actually after retrieval of sequence, they will be BLAST and functionally annotated. These sequence would be genes actually. So I should take already built GUI based Dot-plot and modify it according to my need. I thought that detail will not be required. My apologize if it made problem.


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