Dear Monk,

Here's my exact problem.
I want to find out the positions and the frequency of all possible repeated substrings of fixed length from a given file which looks like this (http://www.ncbi.nlm.nih.gov/nuccore/AC245882.2?report=fasta&log$=seqview&format=text).

eg)$text='ATCGCTATCGC'

For substring of length 3

ATC => Occurred 2 times, at 0 and 6
CGC => Occurred 2 times, at 2 and 8

For substring of length 4

ATCG => Occurred 2 times, at 0 and 6
TCGC => Occurred 2 times, at 1 and 7

and so on..

If I used my script (which I have posted), it would take ages to complete for the above linked file.

if I am not clear yet, please let me know.
 
 


In reply to Re^3: Exact string matching
by saranrsm

in thread Exact string matching
by Anonymous Monk





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