Question: Best Platform For Making Dot Plot
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gravatar for msaadqureshi786
4.7 years ago by
msaadqureshi7860 wrote:

I have to make a Dot plot program ( scpecific 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 retreived.

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 qustion is that what platform would be helpful for me to complete this project?

python java bioinformatics • 2.7k views
ADD COMMENTlink modified 4.7 years ago by Josh Herr5.5k • written 4.7 years ago by msaadqureshi7860
2
gravatar for Josh Herr
4.7 years ago by
Josh Herr5.5k
University of Nebraska
Josh Herr5.5k wrote:

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.

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Josh Herr5.5k

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.

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by msaadqureshi7860
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