Tool:I-PV: a CIRCOS module for interactive protein sequence visualization

Question

[Ibrahim Tanyalcin]

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: [e-mail] || [e-mail] || [e-mail]

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

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Edit - February 5 2018: I had a recent case with someone using ubuntu having problems with relative paths as seen in here. I was not able to reproduce this behavior. If anybody else could please let me know.

[Ibrahim Tanyalcin]

[Ibrahim Tanyalcin]

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

[Ibrahim Tanyalcin]

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

[Ibrahim Tanyalcin]

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,

Answer 1

[Ibrahim Tanyalcin]

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:

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

[Ibrahim Tanyalcin]

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,

Answer 2

[Ibrahim Tanyalcin]

I-PV now accepts a JSON config file as input as well as interactive CLI. The JSON config option allows you to automate image generation. Many fields that were compulsory are now optional.

You only need a fasta file of amino acid sequence and an mRNA fasta file spanning that sequence. A minimal config JSON looks like below:

    {
    "path": "  config  ",
    "proteinFileName": "testInput/fasta.txt",
    "mrnaFileName": "testInput\\mRNA.txt",
    "name": "NFKB",
    "domains": [
        {
            "start": 50,
            "end": 126,
            "name": "domain_X",
            "color": "vdred"
        }
    ]
  }

You can read all the available options here.

If you do not want to deal with dependencies, a docker image does exist as well.

You can find the image in the docker hub.