Find Repeats In A Sequence
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10.3 years ago
Wang ▴ 30

I want to find every repeats codon sequence in DNA sequences using Python so, if i input the sequence, find repeat type and time. absolutely USING PYTHON

Thanx to guys!!!

sequence repeats python homework • 10k views
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4
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This looks like a homework assignment, is it? I think this has something to do with regular expression, and Perl handles it well, too.

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0
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You don't need Perl to use regular expressions. They are two very different languages.

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0
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Do you mean SSR?

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9
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10.3 years ago
Fucitol ▴ 140

It's very easy to do in python using the count function:

from itertools import product    
[sequence.count(''.join(codon)) for codon in product('ATCG', repeat=3)]

Or get the results in a dictionary (you can figure out how to get the max etc yourself):

dict(("".join(codon), sequence.upper().count(''.join(codon))) for codon in product("ATCG", repeat=3))

(edited after brentp's correct comment below)

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2
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+1. Minor nitpick, to get the results in a dictionary, you'd use: dict(("".join(codon), seq.count(''.join(codon))) for codon in itertools.product("ATCG", repeat=3))

otherwise, you get a list of dictionaries of length 1.

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0
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Nice solution; with the caveat that it should be 'atcg' to work for the example sequence given in the question.

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0
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You are correct Neil, that's the risk of having a Python session already open with some sequence data loaded. For safety, you can also use: sequence.upper().count(...) which works on both lower and uppercase data.

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3
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10.3 years ago

Should we really accept doing homework assignments?

A simple invitation to use:

  • help(str)

would have given 'wang' all the basic tools to start this, including:

  • the count() method
  • the join() method
  • the upper() and lower() methods

And he would have learned to use the help() method and the built-in documentation which are fundamental Python tools.

Now he just has a copy-and-paste answer that has taught him nothing...

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