Identifying mutations in an aligment

Question

[Tonor]

Does anyone know of any tools that will identify the mutations present in an alignment?

I have an alignment of hundreds of gene seqs (all closely related), the first sequence in the alignment is the "reference" sequence, and I want to identify and report mutations in the gene seqs with respect to the reference sequence.

The second part, is to identify if those mutations of synonymous/non-synonymous (the gene seqs are coding and are in frame).

Ideally, this would all be command-line based.

[gb]

first, I am not an expert on this. But should you not use something like bowtie and freebayes.

Here some other answers:

Finding Snps From A Bam File

What Methods Do You Use For In/Del/Snp Calling?

[Tonor]

Hi - this is not NGS data - so not SAM/BAM just a standard FASTA alignment of aligned gene sequences

[Andrzej Zielezinski]

I don't think there is a tool for this specific purpose. I'm afraid you will need to write your custom script (e.g. Python/Ruby/Perl) to list the mutations.

Answer 1

[Andrzej Zielezinski]

I think you need to write your custom script for this task. For example, look at the following code in Python:

File: test.py

import sys
from Bio import SeqIO

f = sys.argv[1]

seq_records = SeqIO.parse(f, 'fasta')
refseq_record = next(seq_records)

for seq_record in seq_records:
    for i in range(0, len(refseq_record)):
        nt1 = refseq_record[i]
        nt2 = seq_record[i]
        if nt1 != nt2:
            printseq_record.id, i+1, nt2, nt1)

Alignment in FASTA file (input.fasta):

>seq1
ATGCTGATG
>seq2
ATGCTGACT
>seq3
ACGCT-ATG

Running the script:

python test.py input.fasta

Output:

seq2 8 C T
seq2 9 T G
seq3 2 C T
seq3 6 - G

Columns: (i) sequence identifier, (ii) position in the alignment, (iii) character in this sequence, (iv) character in the reference sequence.

[Tonor]

Thanks - I was going to write something - but thought there would be something already out there

[elisheva]

What you are gonna do in case of insertions?
In that case, the reference sequence also contains gaps, and it is quite problematic to deal with.