Question: Create illustrative image of domains on protein based on position
0
gravatar for guliasitu40
5 weeks ago by
guliasitu4020
guliasitu4020 wrote:

Dear all, My question is regarding the making of an image that will give information about the position of domains on proteins. I have thousands of proteins and for these proteins, we have got the domain type and their position after manual curation from many databases. With this information, I want to make an image that will have all the domains of specific protein with their positions plotted on an image using any programming language viz-R, Python, HTML, etc. Any help in this regards will be highly appreciated.

Protein            Start    End        Domain
**Aco021107 1   1000    Full protein length**
Aco021107   496   702    DUF1336
Aco021107   169    337    START
Aco021107   14  112       PH

Thanks in advance.

ADD COMMENTlink modified 5 weeks ago by Mensur Dlakic6.4k • written 5 weeks ago by guliasitu4020

I read that you are looking for an R approach. if you ran interproscan you would (or can at least ask to) get also generate an image of the domain mappings, no need to do this yourself thus. The image is in SVG if I remember correctly can thus easily be adopted if needed.

ADD REPLYlink written 5 weeks ago by lieven.sterck8.5k

Thanks for your response. The SVG image generated through Interpro gave multiple entries for a single domain. But I want to create a protein domain similar to this image. http://ibs.biocuckoo.org/demo/images/2.jpg (EDC3)

ADD REPLYlink written 5 weeks ago by guliasitu4020
2
gravatar for Mensur Dlakic
5 weeks ago by
Mensur Dlakic6.4k
USA
Mensur Dlakic6.4k wrote:

Haven't tried this, but it seems to be exactly what you want:

https://f1000research.com/articles/7-1105/v1

A very specific solution you may need to fiddle with to suit your needs:

http://rforbiochemists.blogspot.com/2015/11/drawing-protein-domain-structure-using-r.html

The links below do not offer a programmatic solution, but they still may be helpful.

Pfam has its own utility based on JSON to create graphics:

https://pfam.xfam.org/generate_graphic

Other choices:

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Mensur Dlakic6.4k

Thank you very much for your suggestion. The Draw-proteins tool (https://f1000research.com/articles/7-1105/v1) works well for my sequences. I am just exploring possibilities, to change the color of Domain regions.

ADD REPLYlink written 4 weeks ago by guliasitu4020
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