Let's say I have a set of UCSC names of genes.
Is there a database (or databases) I can query through a RESTful request (or something else I can automate on the command line), that would tell me what protein domains are contained in translated genes, such that I could categorize them?
I don't know much about protein databases, so I apologize in advance for what will likely be a n00b question. Thanks for your help.
An easiest way would be to use Biomart. When you select for Attributes, you get an option of choosing information related to Protein Domains and Families. You can then download domain related information from there. They have PFAM, Interpro, TIGRFam data.