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

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?

alignment blast sequence
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updated by Ram Ram • written by Kumar Kumar

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?

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written by andres.firrincieli andres.firrincieli

@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.

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written by Kumar Kumar

1 answer

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

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written by 5heikki 5heikki

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