Multialignment of proteins sequences

Question

[nhungptt17]

Hi guys,

I have a DNA sequence that makes protein 1, but now I'm asked to

• compare the amino acid sequence of protein 1 with nine homologous proteins and make a multialignment of the sequences.
• Determine a consensus sequence for the proteins based on the multialignment.
• Find any specific parts of the proteins that are conserved, then explain why these parts are conserved.

This is part of my report. But I don't know where to start. Can any of you please give me a hint to solve it?

Thanks a lot

Answer 1

[Antonio R. Franco]

• Compare con Clustal Omega. It will give you the consensus
• Look for conserved protein motifs using InterProScan

[nhungptt17]

Thanks a lot Antonio. I used Clustal Omega as you suggest and i made it, the report was submitted.

Thanks :-)

Answer 2

[Abdullah]

You might want to have a look at HMMER for your first request.

[Antonio R. Franco]

I don't know the way is implemented, but the "new" Clustal Omega also works with the Hidden Markov model

[nhungptt17]

Thanks Abdullah. I used Cluster Omega and it worked so i did not look at HMMER. Anyway, thanks a lot for your answer :-)