Wildcard String Comparisons: Set Pattern to a Wildcard Source

chaoticcranium at gmail.com chaoticcranium at gmail.com
Tue Oct 5 21:03:05 CEST 2010

So, I have a rather tricky string comparison problem: I want to search
for a set pattern in a variable source.

To give you the context, I am searching for set primer sequences
within a variable gene sequence. In addition to the non-degenerate A/G/
C/T, the gene sequence could have degenerate bases that could encode
for more than one base (for example, R means A or G, N means A or G or
C or T). One brute force way to do it would be to generate every
single non-degenerate sequence the degenerate sequence could mean and
do my comparison with all of those, but that would of course be very
space and time inefficient.

For the sake of simplicity, let's say I replace each degenerate base
with a single wildcard character "?". We can do this because there are
so many more non-degenerate bases that the probability of a degenerate
mismatch is low if the nondegenerates in a primer match up.

So, my goal is to search for a small, set pattern (the primer) inside
a large source with single wildcard characters (my degenerate gene).

The first thing that comes to my mind are regular expressions, but I'm
rather n00bish when it comes to using them and I've only been able to
find help online where the smaller search pattern has wildcards and
the source is constant, such as here:

Of course, that's the reverse of my situation and the proposed
solutions there won't work for me. So, could you help me out, oh great
Python masters? *bows*

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