Question: SNP Calling of a single bacterial gene
0
gravatar for Mirza.Jawad
12 months ago by
Virtual University of Pakistan
Mirza.Jawad0 wrote:

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.

sequencing snp sequence gene • 395 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by Mirza.Jawad0

So then what will be the next procedure?

ADD REPLYlink written 12 months ago by Mirza.Jawad0

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.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax65k

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

ADD REPLYlink written 12 months ago by cpad011211k
1
gravatar for toralmanvar
12 months ago by
toralmanvar750
toralmanvar750 wrote:

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

ADD COMMENTlink written 12 months ago by toralmanvar750
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