SNP Calling of a single bacterial gene

Question

[Mirza.Jawad]

I have one sequenced bacterial gene (three copies) taken from three different countries. I want to see the SNPs and variant calling (if possible for a single gene) to check out the mutation. I am from NGS background but could not perform SNPs and variant calling analysis yet.
Can we do variant calling for a single gene? How can find the SNPs with having any reference? Later I will go for the structure prediction and the interactions/docking.

[Mirza.Jawad]

So then what will be the next procedure?

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

What format is your data in? Fasta format files? You can use JalView to build multiple sequence alignments and see where the differences are. You can also use MEGA, ClustalW to do the alignments, if you have small number of sequences.

[cpad0112]

do global alignment with softwares like muscle, t-coffee as sequences are short in number.

Answer 1

[Tm]

If your interest is in just one gene, then for first look, you can simply blast them or perform multiple sequence alignment.