Gurus,
I have a list of mutations and I want to see on which domains those mutations are (like kinase, C2, N-terminal, Helicase etc.). And I want them in nice plot like this:
DMDM (http://bioinf.umbc.edu/dmdm/) doesn't get me exactly what I need. I know how to get those domains as a text.
Any help?
Thanks -Kasthuri
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Kasthuri
2 answers
I highly recommend the recently published GPViz software package. It is very simple to use and has all the customization features I have needed.
Download: http://icbi.at/software/gpviz/gpviz.shtml
Manuscript: http://bioinformatics.oxfordjournals.org/content/early/2013/06/19/bioinformatics.btt354.full.pdf
Drop in a gene model file in GTF format, a variant file in VCF format, and a domain model file (human models from Ensembl are available on the GPViz download page) and you are good to go.
If all you need is the domain information, you can search pfam website, for example (http://pfam.sanger.ac.uk/protein/P53_HUMAN). Then, you can map your list of mutation to the domain start and end. For the plot, I found this website from cBio helpful : https://code.google.com/p/cbio-cancer-genomics-portal/wiki/RFC_5_Mutation_Diagrams. Also, I wrote an R script that can give similar plot using grid package (still need to refine). Hope it helps.
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Is this the same question as How To Create Mutation Diagram In R Or In Any Tools?? Is it the data or the plot you're struggling with?
Yes...thanks! I don't want to plot them. I just want to make a quick inspection of the domain compared to the other domains in the gene of interest.
what do you mean with "... of the domain compared to the other domains" ?
I mean the mutations that occur in a particular domain compared with domains where the mutation is not present. Several hotspot mutations occur in, say, kinase domains compared to C2 and other areas of low complexity. Of course, it depends on the gene of interest...