Finding smallest sequence which distinguish any DNA sample

Question

[melihoten]

Hi,

I have 5 different bacteria genome sequences and I need to find smallest sequences which distinguish each of these from other. I need to use R while doing this. Finally, I should get 5 different small sequences,each of them are special and able to distinguish it from others, how can i solve this problem ?

Answer 1

[michael.ante]

This sounds like a homework for me...

The brute force method would be generating all occurring k-mers for each species (k= {1 ... n}) and look for the smallest k where you have unique sequences for each species.

[melihoten]

I am doing an intern right now and Professor asked me to learn that.

How can I perform Brute Force in R ? I couldn't find any package etc. Do you know any way to do it ?

[michael.ante]

Learn R-basics.

Find a package that can count the kmers and install it.

Make a test set (small part of the genomes) to test your approach.

Start with a small k, compare the genomes' kmers, increase k if requested condition not met.