I want to ask if there has some good tools to search the protein domain by sequence and can work as batch input, eg. 1000 hits.
I have some genomic coordinates. All of them are from exon region, we can treat it as coding region.
chr16 68355366 68355614 chr9 71081078 71081471 chr11 77611818 77611831 chr5 139645292 139645415 chr14 105693098 105694607 chrY 22748604 22749732
After I get the DNA sequence, I translate it to protein sequence. There will have 6-frame translation so there will be 6 results for each exon.
Then I need to search if there is any special domain, eg. zinc finger domain in this exon.
Any good suggestions for this process?
Thanks a lot!