[EMBOSS] How to feed the CMA KFERQ motif into fuzzpro

[Peter Rice]

On 09/10/2014 18:01, Aengus Stewart wrote:
>
> I have the 1990 FJ Dice paper that outlines a pentapeptide that targets
> cytosolic proteins for lysosomal proteolysis
>
> The motif is either
>
> [KR][FIVL][ED][RK]Q or Q[RK][ED][FIVL][KR]
>
> However it gets more complicated.  It doesnt matter the order of the 4
> resides before/after the Q.
>
> I have no idea how to write this in a way that will make sense to feed
> into fuzzpro.  I am happy to do multiple runs of fuzzpro and merge
> results but even then.....
>
> I could write a script to feed all possible options to fuzzpro but as I
> am also screening against the whole mouse proteome its going to be messy.

Well, though you can use brute force and write your own application, 
there are still just 12 possible orders with Q at the end, and 12 with Q 
at the start (two residues are [KR]) so you could create a pattern file 
and use fuzzpro -pattern @filename on the command line.

For example (Q at the end only in this file)

%cat cytosolic.pat
 >pat12
[FIVL][DE][KR][KR]Q
 >pat21
[DE][FIVL][KR][KR]Q
 >pat23
[KR][FIVL][DE][KR]Q
 >pat32
[KR][DE][FIVL][KR]Q
 >pat34
[KR][KR][FIVL][DE]Q
 >pat43
[KR][KR][DE][FIVL]Q
 >pat13
[FIVL][KR][DE][KR]Q
 >pat31
[DE][KR][FIVL][KR]Q
 >pat24
[KR][FIVL][KR][DE]Q
 >pat42
[KR][DE][KR][FIVL]Q
 >pat14
[FIVL][KR][KR][DE]Q
 >pat41
[DE][KR][KR][FIVL]Q

Does that help?

Peter Rice
EMBOSS Team