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

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

genome
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updated by Biostar Biostar • written by Abhi Abhi

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

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written by Steve Lianoglou Steve Lianoglou

hehe.. I should add the smallest kmer size

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written by Abhi Abhi

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

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written by Bach • Bach

2 answers

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

enter image description here

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written by Gjain Gjain

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.

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written by Istvan Albert Istvan Albert

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.

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written by Abhi Abhi

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