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?