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