In the file bootcamp_blast.tar.gz I found MotifFinder.java.
It searches sequences for a motiff Symbol by Symbol.
If I am searching 4MB file, that could take awhile.
By contrast, I can search a string very quickly with the indexOf("motiff")
function.
My question:
Is there a better way to search a sequence for a motiff?
Andy Hammer
University of Utah
Human Genetics