How can I remove FASTA sequences with an asterisk inside the sequence?

Question

I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences.

In the example below, I have three sequences:

From this example, I would like to obtain only the following output:

Answer 1

Try seqkit grep

seqkit grep --by-seq --invert-match --pattern '*' seq.fa

--by-seq search by seq

It will output sequences without an asterisk.

Answer 2

It’s good you brought up the question.

* are stop codons

Don't simply parse out the * symbol. If done incorrectly, it could constitute 'tampering' and that’s a red line in biology.

The * means a stop codon in the middle of a protein sequence. There are quite a number of reasons why there is an *, i.e., a stop codon in the sequence, for example, in no particular order:

• the open reading frame is out of frame which is part of the natural molecular biology, i.e., there can be multiple reading frames in a gene
• the open reading frame is out of frame due to a sequencing error and poor annotation (which is common);
• the wrong reading frame was used (very, very common);
• the locus isn't translated, e.g., it’s an intron or UTR (untranslated region)

The list goes on, e.g., it could be expression regulation ...

---

1. If it is not an intron/UTR the way you might 'remove' * is by changing the reading frame, e.g., try using the second codon position (then the third) as the opening reading frame: if the * 'disappear' it was very likely just a reading frame issue. How to do that is a separate question. The resulting amino acid sequence will of course be very different.

2. There's a second possibility if the reading frame is correct, which is to treat each locus between the * as a separate protein. That way the * is 'removed' because their a multiple proteins within the locus. In that case, a \n would replace the * (Mac and Linux), i.e., carriage return.

Answer 3

You could use Biopython for this. It makes FASTA parsing really easy.

'''
Python version: 3.10.0
Biopython version: 1.79
'''
from Bio import SeqIO
for seq_record in SeqIO.parse("input.fasta", "fasta"):
    if "*" not in (seq_record.seq):
        print(">",seq_record.id)
        print(seq_record.seq)