matching and counting strings (k-mer of DNA) in R

Question

I have a list of strings (DNA sequence) including A,T,C,G. I want to find all matches and insert into table whose columns are all possible combination of those DNA alphabet (4^k

Answer 1

Another way to do this:

DNAlst<-list("CAAACTGATTTT","GATGAAAGTAAAATACCG","ATTATGC","TGGA","CGCGCATCAA","ACACACACACCA")
len <- 4
stri_sub_fun <- function(x) table(stri_sub(x,1:(stri_length(x)-len+1),length = len))
sapply(DNAlst, stri_sub_fun)
[[1]]

AAAC AACT ACTG ATTT CAAA CTGA GATT TGAT TTTT 
   1    1    1    1    1    1    1    1    1 

[[2]]

AAAA AAAG AAAT AAGT AATA ACCG AGTA ATAC ATGA GAAA GATG GTAA TAAA TACC TGAA 
   1    1    1    1    1    1    1    1    1    1    1    1    1    1    1 

[[3]]

ATGC ATTA TATG TTAT 
   1    1    1    1 

[[4]]

TGGA 
   1 

[[5]]

ATCA CATC CGCA CGCG GCAT GCGC TCAA 
   1    1    1    1    1    1    1 

[[6]]

ACAC ACCA CACA CACC 
   4    1    3    1