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btd_kmer

K-mer counts of number of occurences of given DNA word/substring

Calling Function

y = btd_kmer(x1, x2)

Arguments

x1

String of single-letter codes specifying a DNA sequence

x2

DNA word/substring length.

y

Counts of DNA word/substring (Nx2 matrix of text: y(:1) are words names; y(:,2) are respective count numbers).

Description

y = btd_kmer(x1, x2) count the number of occurence of a particular substring that are 1,2,3...n-1 nucleotides long in a given DNA sequence b.

Examples

y = btd_kmer("ATCGATCGATCGTATATGCTAGCTA", 2)
evstr(y(:,2))'
--> y = btd_kmer("ATCGATCGATCGTATATGCTAGCTA",2)
 y  = 
!CG  3  !
!AT  3  !
!TA  2  !
!CT  2  !
!TG  1  !
!AG  1  !

--> evstr(y(:,2))'
 ans  =
   3.   3.   2.   2.   1.   1.

See Also


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