As a humble seeker of assistance... I am looking to generate a script that returns the frequency of a short word in a longer original (a DNA sequence).... I have a one-liner for generating all possible short words of a certain length (k), e.g.; 
perl -se '$,="\t"; print split / /, qx/echo @{["{$a}" x $k]}/;' -- -k=
+4 -a='A,T,G,C'

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This gives 256 tab delimited short DNA sequences. I would like to use these as column names, and score the frequency of each short DNA sequence in a set of longer sequences, e.g. 
                 ACTG    ATTG    ATGC   etc
ATGCTGTACTG        1      0        1
ATGATGATCTG        0      0        0
ATGCGTATGCA        0      0        1
ATGCTAGACTG        1      0        1

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The files are >20000 lines, and it would be nice to scale to larger short word sizes (i.e. 7 letter words such as'AGTGTAT' would generate >16000 columns for every combination), so efficiency is fairly important. Unfortunately I haven't been able to find a ready made example to do precisely what is required. Any guidance to this would be much appreciated. Thanks.

In reply to Find number of short words in long word by sedm1000

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