Conserved domains in multiple sequence alignment
Dear all,
I have few protein sequences (belongs to a protein family) from different algae which I have aligned using mafft. I want to know the conserved domains in the aligned sequences, so that I can make some biological inference by looking at the presence or absence of certain domains in the protein family. I have searched and found Msavis
"https://agbase.arizona.edu/tools/MSAVis.html".
I want to know if any other tool is also available for this purpose.
Please help
Thanks in advance
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siu
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You could compare your sequences with conserved domains from a database like Pfam. It contains HMM profiles of protein domains. The simplest would be to run
hmmsearch(from HMMER) of the Pfam-A database against your sequences. This would report matching domains for each sequence individually. If you think your alignment would help identifying the domains, you could then build a profile out of it (run hmmbuild on your alignment), and then, use a tool designed to compare profiles directly.