Find Repeats In A Sequence

Question

[Wang]

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!!!

[Vitis]

This looks like a homework assignment, is it? I think this has something to do with regular expression, and Perl handles it well, too.

[veronicaschroeder78]

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

[Renm79]

Do you mean SSR?

Answer 1

[Fucitol]

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)

[brentp]

+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.

[Neilfws]

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

[Fucitol]

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.

Answer 2

[Leonor Palmeira]

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...