ClustalOmegaCommandline issue (alignment issue)

Question

[benjamin]

Hi all,

I'm actually using the ClustalOmegaCommandline package and everything is working except that the aligned sequence output is completly wrong. Indeed, when I run the programme on python3 I get an alignment such this one:

ok SingleLetterAlphabet() alignment with 2 rows and 1625 columns CEHNTAGRDCEKCLDFYNDAPWGRASPTNVHECKACNCNGFSNK...--- pro1 MGGKIAAILLFAFFTSGSRSEPDFVDGQFNKINKNRVEVKCYDD...LEP pro2

And I know that it should not be aligned like that; the above sequence should be aligned further in the frame (in other word we sould not see the AA in the display, but only "-")

Here is my code:

from Bio.Align.Applications import ClustalOmegaCommandline

in_file = "/Users/etudiant/Desktop/Horizon_project/busco/Divergence/prot_ali" out_file = "/Users/etudiant/Desktop/Horizon_project/busco/Divergence/output_alignment.fasta"

def align_v1 (Fasta):

clustal_cline=ClustalOmegaCommandline(infile=Fasta, outfile=out_file)
stdout, stderr = clustal_cline()

MultipleSeqAlignment = AlignIO.read(out_file, "fasta") 
print ("ok",MultipleSeqAlignment)

align_v1(in_file)

Does anybody has a solution for me?

thanks

[Jean-Karim Heriche]

Without seeing the sequences, it's hard to say anything. Have you tried aligning them using something else, e.g. web-based clustal omega or the command line tool directly ? One possibility is that your python wrapper doesn't actually do anything, possibly because it doesn't find/run clustalo (the Clustal Omega program) so check that you have clustalo installed and findable by your python script.

[GenoMax]

benjamin.guinet : Please don't delete posts when they have at least one comment/answer. If you found a solution on your own post it as an answer so it can be useful to others in future.

Answer 1

[benjamin]

Hi, finnaly I resolved my problem. I used the wrong format (my file was not in fasta format) and the alphabet was wrong as well, I had to add alphabet=IUPACProtein from Bio.Alphabet.

Thanks all for your help.