Question: Unique Shortest Kmer Size For It To Be Unique In The Genome
3
gravatar for Abhi
6.9 years ago by
Abhi1.5k
United States
Abhi1.5k wrote:

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 • 2.6k views
ADD COMMENTlink modified 4.3 years ago by Biostar ♦♦ 20 • written 6.9 years ago by Abhi1.5k
1

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

ADD REPLYlink written 6.9 years ago by Steve Lianoglou5.0k
1

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

ADD REPLYlink written 6.9 years ago by Bach540

well played ... touché ;-)

ADD REPLYlink written 6.9 years ago by Steve Lianoglou5.0k

hehe.. I should add the smallest kmer size

ADD REPLYlink written 6.9 years ago by Abhi1.5k
2
gravatar for Gjain
6.9 years ago by
Gjain5.3k
Göttingen, Germany
Gjain5.3k wrote:

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

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by Gjain5.3k
2
gravatar for Istvan Albert
6.9 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

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.

ADD COMMENTlink written 6.9 years ago by Istvan Albert ♦♦ 79k

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.

ADD REPLYlink modified 6.9 years ago • written 6.9 years ago by Abhi1.5k
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