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
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