Suggestion for new use for EMBOSS program

Per Johansson heme at
Thu Nov 7 12:05:55 UTC 2002

I have it difficult to find a replacement for the GCG program
FINDPATTERNS. The EMBOSS program fuzznuc cannot use a database of
patterns (primers). Other alignment programs in EMBOSS like
supermatcher are useful but, among other things, you can't choose
mismatch settings. 

The best replacement I've found is the EMBOSS program tfscan! Tfscan
uses a database of patterns, but you can't reverse the patterns (you
have to put in copies of forward and reverse primer sequences in the
database). The tfscan algorithm is ideal (and is much faster than find
patterns) but obviously a few minor changes to the input and output
would be required if it were used in a replacement program.

Obviously, I could write a script to wrap tfscan but I'd like to
avoid this.  A new program with this functionality would be beneficial
for the EMBOSS package.


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