Comments on: Visualization of internal repeats in proteins (or DNA)

By: Bioinformatics Zen » February 2008 edition of Bio::Blogs

Bioinformatics Zen » February 2008 edition of Bio::Blogs — Sat, 15 Mar 2008 15:02:14 +0000

[...] Butter, What You’re Doing, and BBGM. Pawel Szczesny became a Freelance Scientist, and posted a novel method for visualising repeats in sequences. Stew showed how to increase MySQL speed, and Biocurious had a biohumorous article [...]

By: wrightfisher

wrightfisher — Fri, 01 Feb 2008 18:27:36 +0000

This visualization reminds me of the RNA structural diagrams which indicate base pairing partnerships. Excellent examples appear in the published writings of E. Rivas and S.R. Eddy.

By: freesci

freesci — Wed, 30 Jan 2008 21:09:22 +0000

Hi Paulo, the script is very crude, so I don’t plan to make it freely available, although I may send it upon request.

By: Paulo Nuin

Paulo Nuin — Wed, 30 Jan 2008 21:02:17 +0000

Hi Paweł

Would you distribute the script that generate the visualization? If so drop me a note.

Cheers

By: ignasi

ignasi — Sat, 26 Jan 2008 14:56:15 +0000

Well, I have to represent some protein sequences and subsequences of them of at least 5 different types after some analyses and predictions.
I’ve been looking for graphical tools in Perl (my scripts are actually in perl). I’ve found the GD library and some mods in BioPerl which are more or less what I want. But I’d like it to be interactive as well so when passing the pointer over the graphic for instance, it could display some values or the actual sequence bit or whatever… Not just plain pictures, which should also be available for larger analyses rather than single sequence runs. And also this, a way to represent many sequences and its information…but I guess this is an information visualization problem of an “omics” approach.
And this you mention that in a website should work as an applet it’s important since this work has as a goal, build a web service… But if you display an output like a picture, it can be generated also in the server and then sent back, or what?
thanks!

By: rascunho » Blog Archive » links for 2008-01-25

rascunho » Blog Archive » links for 2008-01-25 — Fri, 25 Jan 2008 20:27:29 +0000

[...] Visualization of internal repeats in proteins (or DNA) « Freelancing science This fitted my requirements so I’ve implemented it with some help of Processing (and which I’ve added later to a protein analysis server that has a chance to be published next month). Resulting visualization is below: (tags: freesci.wordpress.com 2008 mes0 dia25 at_tecp visualization protein processing biology bioinformatics bioinformática blog_post) [...]

By: freesci

freesci — Thu, 24 Jan 2008 17:26:27 +0000

I don’t know Java almost at all, but still I can code something in Processing (it’s pretty easy to learn if you know at least one programming language). So learning curve of Processing may be not an issue. More important thing is that with Processing you cannot create a graphics without popping out a window with it. So in other words, it’s unusable if you plan to do some stuff through a web server/remotely executed script (you may include it as an applet in the webpage, which is what I did, but keep that in mind). Other than that it’s probably the best choice currently for preparing sophisticated output in a reasonable time in terms of coding (Processing script that generates above graphics is around 100 lines, including defining variables, reading/parsing input file, setting the sizes, legend etc.).

For python I would recommend PIL (Python Imaging Library) and matplotlib. However, if you would specify a little bit what you are aiming for, probably I could come up with different recommendations.

By: ignasi

ignasi — Thu, 24 Jan 2008 17:12:23 +0000

Simply beautiful. Processing is an amazing language.
By the way, do you recommend it for nice “bioinformatics outputs”? I’ve got to do some work that has an important part on the graphical output… and I’m strongly considering using processing, although I’m afraid of the learning curve it has. I jnow nothing about java but I’m getting into OOprogramming with python right now…
Any advice? Thanks a lot.