Generating a consensus sequence of a large number of amino acid sequences in python

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2.0 years ago

unicorn2kang • 0

Hi,

I want to generate a consensus sequence of a large number of amino acid sequences using python.

For example,

If there are three different amino acid sequences:

   MAHEDYIG ... HLY
   MAAEDYLP ... HLY
   MAHEDYIG ... TLY

Then MAHEDYIG ... HLY has to be generated as a consensus sequence.

Could anyone create python code for this algorithm? I want to put FASTA file, which is aligned with Multiple Sequence Alignment tool, in the code and want to put a specific weight for each conserved residue.

consensus msa sequence • 1.0k views

ADD COMMENT • link 2.0 years ago by unicorn2kang • 0

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If I understand you properly you are trying to generate the consensus sequence after running MSA?

See: Consensus sequence software?

ADD REPLY • link 2.0 years ago by iraun 6.2k

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Yes! I've used MUSCLE/Clustalw/Clustalomega packages for running MSA but I am struggling with generating consensus sequence since I cannot find any packages for it in python.

ADD REPLY • link 2.0 years ago by unicorn2kang • 0

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