Question: Aligning Protein Seq multifasta
0
gravatar for maximilian.mayerhofer
14 months ago by
maximilian.mayerhofer20 wrote:

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 • 425 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by maximilian.mayerhofer20

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.

ADD REPLYlink written 14 months ago by jrj.healey12k

How do I see if the translation was correct?

ADD REPLYlink written 14 months ago by maximilian.mayerhofer20

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

ADD REPLYlink written 14 months ago by jrj.healey12k

Does more multi.fasta show properly formatted protein sequence?

ADD REPLYlink written 14 months ago by genomax65k

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

ADD REPLYlink modified 14 months ago • written 14 months ago by jrj.healey12k
2
gravatar for maximilian.mayerhofer
14 months ago by
maximilian.mayerhofer20 wrote:

Update:

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

ADD COMMENTlink written 14 months ago by maximilian.mayerhofer20
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