What is the difference between Average Nucleotide Identity (ANI) and blastn analysis?

Question

[Kumar]

I did the pan-genome analysis, from which I got the core, accessory, and unique gene sequences. Now, I need to know specifically which are strains shared more genes among them in the accessory gene cluster. Hence, I opted for a strategy, where I firstly extracted all the gene sequences for each strain from accessory gene cluster and saved them in a single fasta file. Then I did ANI analysis, based on the ANI value shall I consider that the Top ANI value showed pairs are shared more genes among them? or should I go for blastn? I need to know, what is the difference between ANI and blastn?

[andres.firrincieli]

Now, I need to know specifically which are strains shared more genes among them in the accessory gene cluster.

Why don't you run a cluster analysis on the accessory gene cluster frequency table (binary matrix 1,0 aka presence,absence) to find which strains share a similar accessory pan-genome?

[Kumar]

@andres.firrincieli I have used BPGA pipeline for my analysis, in which output does not have the following files. accessory gene cluster frequency table (binary matrix 1,0 aka presence,absence). In BPGA I can obtain core sequences, accessory sequences and unique sequences as three individual files. All the strain sequences are clustered in a single individual file, that is where I am facing this problem.

Answer 1

[5heikki]

Blastn is a tool for local nucleotide sequence alignments. ANI generally refers to average nucleotide identity over entire genomes (global)