Solve LING Linguistic Complexity of a Genome

weka511 / bioinformatics

Code inspired by Bioinformatics Algorithms: an Active Learning Approach.

GNU General Public License v3.0

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Solve LING Linguistic Complexity of a Genome #23

Open weka511 opened 5 years ago

weka511 commented 4 years ago

Too slow at present

weka511 commented 4 years ago

I have just timed the loop:

 for i in range(len(string)):
        for j in range(i,len(string)):
            pass

which requires 21 m 46.51 s for a string of length 89799, so there is no way a naive Trie is going to give an answer within 5 minutes. Can we chunk string somehow?

weka511 commented 3 years ago

I'll leave tis open until I understand Ukkonen's algorithm