Question: Multialignment of proteins sequences
0
gravatar for nhungptt17
4.0 years ago by
nhungptt1720
Norway
nhungptt1720 wrote:

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 dont know where to start. Can any of you please give me a hint to solve it?

Thanks a lot,

 

bioinformatic • 1.2k views
ADD COMMENTlink modified 4.0 years ago by Abdullah100 • written 4.0 years ago by nhungptt1720
0
gravatar for Antonio R. Franco
4.0 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.2k wrote:

- Compare con Clustal Omega. It will give you the consensus

- Look for conserved protein motifs using InterProScan

 

ADD COMMENTlink written 4.0 years ago by Antonio R. Franco4.2k

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

Thanks :-)

 

ADD REPLYlink written 4.0 years ago by nhungptt1720
0
gravatar for Abdullah
4.0 years ago by
Abdullah100
Germany
Abdullah100 wrote:

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

ADD COMMENTlink written 4.0 years ago by Abdullah100

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

ADD REPLYlink written 4.0 years ago by Antonio R. Franco4.2k

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

ADD REPLYlink written 4.0 years ago by nhungptt1720
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