Aligning Protein Seq multifasta

Question

[maximilian.mayerhofer]

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

[Joe]

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.

[maximilian.mayerhofer]

How do I see if the translation was correct?

[Joe]

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

[GenoMax]

Does more multi.fasta show properly formatted protein sequence?

[Joe]

less is more ;) https://en.wikipedia.org/wiki/Less_(Unix)

Answer 1

[maximilian.mayerhofer]

Update:

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