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Aligning Protein Seq multifasta

So,

I have got a multifasta-file

>strain 1
ATCGCTCGACTG
>strain 2
ATGCGCAGCGAC
.....

I translate this to Protein using EMBOSS. And I have a short Domain sequence of that Protein in AA that I want to align to see if there are any mutations in there. So i use cat to align both files in one.

cat multi.fasta shortseq.fasta>combined.fasta

Using MAFFT, I do not get a usable Output (big gaps). 

mafft --reorder --adjustdirection combined.fasta>combined.aln

Should I use a different Approach for aligning?

Best Regards,

Max

alignment
• 2,207 views • link
written by maximilian.mayerhofer • maximilian.mayerhofer

Try clustal omega, its supposed to work nicely for protein sequences in particular.

Have you checked your fasta file is correct? Make sure the translation has worked properly.

• 0 views • link
written by Joe Joe

I mean literally read the fasta file and make sure it's not just ATCG..

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written by Joe Joe

Does more multi.fasta show properly formatted protein sequence?

• 0 views • link
written by GenoMax GenoMax

1 answer

Update:

I used the wrong translation table, therefor, the translation was flawed. After correction, mafft was useful again.

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written by maximilian.mayerhofer • maximilian.mayerhofer

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