Question: What is the difference between Average Nucleotide Identity (ANI) and blastn analysis?
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gravatar for Kumar
5 weeks ago by
Kumar40
India
Kumar40 wrote:

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?

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by Kumar40

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?

ADD REPLYlink written 5 weeks ago by andres.firrincieli1.1k

@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.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Kumar40
2
gravatar for 5heikki
5 weeks ago by
5heikki9.3k
Finland
5heikki9.3k wrote:

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

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by 5heikki9.3k
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