|Perl: the Markov chain saw|
Re^4: Comparing a large set of DNA sequencesby roboticus (Chancellor)
|on Nov 10, 2011 at 18:39 UTC||Need Help??|
Yes, this method breaks down pretty quickly when the criteria are relaxed much. But I found a nifty variation that's a little bit more flexible (and still very limited): Rather than replace the character with an asterisk, we can remove the character entirely. That way, not only will it match a single wildcard position, but would allow it to find some two-character differences (such as a character deleted or inserted in two different locations). I need to find a simple way to group the replicated matches before I'm happy with it.
I'm still playing around with it, but I'm at work and need to get stuff done. So I'm posting what I have so far, just in case I never get back around to it:
I'd like to eliminate the duplicate groups, probably by building another hash from the original results. But I haven't figured out a nice way to do so yet.
When your only tool is a hammer, all problems look like your thumb.
Update: Minor formatting & text update.