Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
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gravatar for Ibrahim Tanyalcin
2.2 years ago by
Belgium
Ibrahim Tanyalcin870 wrote:

Abstract

Summary: Today’s genome browsers and protein databanks supply vast amounts of information about proteins. The challenge is to concisely bring together this information in an interactive and easy to generate format.

Availability and Implementation: We have developed an interactive CIRCOS module called i-PV to visualize user supplied protein sequence, conservation and SNV data in a live presentable format. I-PV can be downloaded from http://www.i-pv.org.

Contact: itanyalc@vub.ac.be || ibrahim.tanyalcin@i-pv.org || support@i-pv.org

Supplementary Information: Please refer to the supplementary section and http://www.i-pv.org .

 

Note: The article is published at:

Bioinformatics: http://bioinformatics.oxfordjournals.org/content/early/2015/10/10/bioinformatics.btv579.abstract

DOI: 10.1093/bioinformatics/btv579

ADD COMMENTlink modified 7 months ago • written 2.2 years ago by Ibrahim Tanyalcin870
3

Roadmap of some features

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Ibrahim Tanyalcin870
2

Added a lot of new features:

-ability to color regions, variations

-ability to filter variants of certain interest

-ability to see cDNA information

-ability to extract cDNA between any two residue with customizable number of characters per line.

-updated the github page: https://github.com/IbrahimTanyalcin/I-PV

You can find a live example here: http://i-pv.org/EGFR.html And also here is the last tutorial video for changing colors: http://i-pv.org/intro_ipv_alt5.html

ADD REPLYlink modified 20 months ago • written 22 months ago by Ibrahim Tanyalcin870

For those that are interested in seeing the code online for EGFR sample, you can visit this gist: https://bl.ocks.org/IbrahimTanyalcin/4909088ce481cb0b05ecfe7d2ee8145d

ADD REPLYlink modified 7 months ago • written 16 months ago by Ibrahim Tanyalcin870

Dear Biostars Community,

I-PV is now on thinkable.org . If you'd like to support the project for further development, you can vote from the link.

Thank you,

ADD REPLYlink written 4 months ago by Ibrahim Tanyalcin870
0
gravatar for Ibrahim Tanyalcin
7 months ago by
Belgium
Ibrahim Tanyalcin870 wrote:

I am extending I-PV with a new add-on called INDORIL. This add-on will enable you to look at your point mutations in a user defined 3D coordinates. You can either use the built in metrics or upload your custom data.

I have written an experimental svg 3D renderer about 2.5 years ago but never had the chance to go back and make some improvements. Now the fps is improved a bit, you can export values to third party software or construct basic shape primitives. Here is what the software looks like:

INDORIL output

To get a better idea what the software can do you can also watch THIS tutorial:

If you need to first learn how to generate these plots you can look over HERE:

To check live examples visit the WEBSITE

The reference: http://biorxiv.org/content/early/2017/06/09/148122

ADD COMMENTlink modified 6 months ago • written 7 months ago by Ibrahim Tanyalcin870

Dear Biostars Community,

I-PV and INDORIL is now on thinkable.org . If you'd like to support the project for further development, you can vote from the link.

Thank you,

ADD REPLYlink written 4 months ago by Ibrahim Tanyalcin870
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