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

[Aengus Stewart]

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.

Anyone got suggestions?


Cheers
Aengus

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Aengus Stewart                                 Tel: +44 (0)20 7269 3679
Head of Bioinformatics and BioStatistics
CRUK London Research Institute
Lincoln's Inn Fields, Holborn, London, WC2A 3LY, UK
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