Question: SNP frequencies in Fasta Alignment
0
gravatar for akhilvbioinfo
3.1 years ago by
akhilvbioinfo140
India, chennai
akhilvbioinfo140 wrote:

Hai everyone

I have a set of fasta aligned file from this alignment file how i will get snps and its frequencies

snp alignment fasta • 1.1k views
ADD COMMENTlink modified 3.1 years ago by Fabio Marroni2.4k • written 3.1 years ago by akhilvbioinfo140

Hi! In general, the more detail you provide, the higher is the chance that someone can help you. For example:

1) What do you mean by "fasta aligned files"?

2) How did you align them and what do they represent?

3) Do you have one fasta file for each individual you sequenced?

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Fabio Marroni2.4k

i aligned 20 genes (fasta format) using MAFFT and i want to find gene variation respect to snp/snp frequencies

ADD REPLYlink written 3.1 years ago by akhilvbioinfo140
0
gravatar for Fabio Marroni
3.1 years ago by
Fabio Marroni2.4k
Italy
Fabio Marroni2.4k wrote:

For any position do this:

1) Count all the different nucleotides (I assume for simplicity there are only two kinds, A and G).

2) Count how many As, count how many Gs.

3) The frequency is e.g. As/(As+Gs).

Repeat for all the positions.

ADD COMMENTlink written 3.1 years ago by Fabio Marroni2.4k

Is there any programmes or tool to calculate this

ADD REPLYlink written 3.0 years ago by akhilvbioinfo140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1003 users visited in the last hour