Question: NGS result with alteration: how to find whether the alteration will bring amino acid substitution?
gravatar for n.e.coli.1822
5.0 years ago by
n.e.coli.18220 wrote:

Hi there, I ask a favour to you.

I had NGS with 4 bacteria, to say S1, S2, R1, R2 with a reference F.

Each of the alteration results are based on the compare to F.

What I`m going to do is,

1. comparing the alteration difference between S and R and

2. to check the alterations of R compared to S, changed the amino acid of the site; yes, to find the type of mutation whether it is a synonymous or non-synonymous​ mutation.

I've solved the question 1. by myself with simple functions of excel.

By the way, it is too large amount of data and complicated functions are needed to do with excel.

So, I beg your help.

I`m finding tools or any methods that can do

1. changing a genome sequence with listed alteration on excel or

2. one blackmagic-like tool that fit for my situation.

Thank you for your warm-hearted favour!

snp open ngs • 966 views
ADD COMMENTlink modified 5.0 years ago by Devon Ryan98k • written 5.0 years ago by n.e.coli.18220
gravatar for Devon Ryan
5.0 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

You'll do yourself a favor by not using Excel for any of this.

For comparing variants you can use things like VCFtools. For annotating them you can have a look at snpEFF or "variant effect predictor", which is from Ensembl.

ADD COMMENTlink written 5.0 years ago by Devon Ryan98k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1901 users visited in the last hour