Finding Conserved Protein Domains
I have a nucleotide sequence given to me for my homework and need to find if the gene the sequence codes for has any conserved domains. I need to find multiple non-overlapping protein domains. How do I go about doing this? What online search programs could I use?
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I would start with hmmscan: https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan
Copy past your sequence into interproscan , you should get everything you need.
Edit: The online version doesn't accept the nucleotides, so you must convert first your sequence ...
You can also copy & pase your DNA sequence to Pfam. A six-frame translation of your DNA will be performed automatically, then each frame will be searched for protein domains.