Simple tools for creation of figures of gene and protein structure

Question

[andre.arrudalima]

Is there an online/simple and free tool for creating figures of gene and protein with its features/domains? Simple figures, like a bar representing the gene?protein and smaller bars inside it representing motifs/domains.

Thank you

[Pierre Lindenbaum]

you asked the very same question one year ago. Online tool for creating figures of gene with its features

[andre.arrudalima]

Yes, but all the answers on the pages that you linked me are 9+ years old. But thank you anyway

Answer 1

[Mensur Dlakic]

There is a whole list of programs in that group:

https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Protein

Not in the list:

https://github.com/LKremer/showTree

Up until a month ago this was working (I used it for a recent paper), but not any more:

http://pfam-legacy.xfam.org/generate_graphic

The closest replacement for that functionality:

https://github.com/ProteinsWebTeam/domain-gfx

Answer 2

[Alex Reynolds]

UCSC Genome Browser

Answer 3

[fileyfood]

Yes, check out the Genomics 2 Proteins portal. The tool allow you to map any feature, including domains onto a protein structure and capture high resolution images of both the features in sequence and structure.

You should also check out the UniProt Structure viewer and RCSB PDB Sequence Structure viewer. These won't let you capture a high resolution image of the sequence, but will for the structure. You may not be able to highlight all domains with these, but you could highlight 1 domain at a time in each of these tools and capture a high resolution image.

Offline, you can use the PyMOL viewer. You will need to annotate the domains though, so this may not address your needs.