kmers

A place to play around with kmers

max kmers in a seqeunce

max_kmers = (L-k)+1

Sequence of 50nt for 3mers

max_kmers = (50-3)+1 max_kmers = 48

proof

sliding window over sequence L=10 can collect each 3mer (10-3)+1 = 8

0 CATGTCGATG 1 CAT 2 ATG 3 TGT 4 GTC 5 TCG 6 CGA 7 GAT 8 ATG

how many combinations of ATCG in kmer

alphabet = (ATCG) = 4

4^3 = 64 64 3mers

4^1=4 4^2=16 4^3=64 4^4=256 4^5=1024 4^6=4096

splitting a sequence for multithreading

Sequence length should be significant, say 1000 or more

CATCGATGCTAGC

To get all kmers without overlap or missing anything, split the sequence with an overlap of kmer-1

So for k=3

CATCGATGCTAGC CATCGA CAT ATC TCG CGA GATGCTAGC GAT ATG TGC GCT CTA TAG AGC

merging multithreaded KmerData

vectors can be pre-allocated with capacity using the local sequence length still, but move scoring to the end if each sequence comes with the break position (end pos of last seq -2) Then record positions as normal then during the merge, just append them all to one vector and sort it, smallest to largest. Then do the score calculation