[EMBOSS] Help to build a motif for fzzpro

[Guy Bottu]

	Dear Aengus,

I have an idea of how to do it. You must of course complete the 
motif/pattern as much as possible because with just {DE}(4) you will 
find much to much unless you search only a few sequences. You must run 
the program fuzzpro with parameter -rformat=listfile. You will obtain as 
output an EMBOSS list file. You can then run fuzzpro again with as 
sequence input list::xxx (xxx the name of your file) and as pattern 
input @yyy where yyy contains :

 > basic_1
<[HKR].
 > basic_2
<x-[HKR].
 > basic_3
<x-x-[HKR].
 > basic_4
<x-x-x-[HKR].

Indeed, the input will contain only sequence fragments matching the 
pattern and the basic amino acid hence should be in one of the first 4 
positions.

	Regards,
	Guy Bottu,
	ex-collaborator of the Belgian EMBnet Node