Can anyone help me how to draw domains of proteins? which software i can use? I am looking for a tool that can plot a protein domain structure (similar to how it is done in Pfam or Smart) .
if you run your proteins through InterproScan you will get be default an image as output which shows the location of the domains on your input protein.
Have a look at the drawProteins package on Bioconductor or at the seqvisr package on GitHub.
If you want Pfam-like domain representations, their site has as option to do it. One has to enter domain boundaries, colors, the style and simply click "Generate graphic."
ProSIte also does a nice job:
tools mentioned by other users are great, a couple more tools here https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Protein
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