Unique Shortest Kmer Size For It To Be Unique In The Genome

Question

[Abhi]

Hey Guys

I am not recollecting the math to find the kmer length that will be unique , given a genome size... How does this change for a metagenome..I guess there is no real way to estimate it for metagenomes right as the genomic space is quite large ?

Thanks! -Abhi

[Steve Lianoglou]

A kmer that's (length_of_genome / 2) + 1 NT long guaranteed to be unique ;-)

[Bach]

No, it is not. Simple example: "AAAA" as genome. I do agree though that this example is a bit far fetched :-)

[Steve Lianoglou]

well played ... touché ;-)

[Abhi]

hehe.. I should add the smallest kmer size

Answer 1

[Gjain]

Hi Abhi,

I think this paper will answer your question:

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

Answer 2

[Istvan Albert]

I think that there is no such formula beyond of what Steve said.

At best you can estimate the probability of observing a certain kmer provided the genome or data was randomly sampled from a certain base distribution.

[Abhi]

I agree Istvan..so to rephrase it..I am looking for a kmer size given a genome size that you would expect it to map randomly to the genome with a very low probability say (10^ -3 or low). I did find some text about this but haven't had a chance to go through it in detail. Once I am done I will post about it.