A good example of a complete and concise protocol for ORF finding (from one of our students):

PROTOCOL
a) SMS ORFinder / forward strand / frames 1, 2 & 3 / min 60 AA / 'any codon' initiation / 'standard' genetic code
b) SMS ORFinder / reverse strand / frames 1, 2 & 3 / min 60 AA / 'any codon' initiation / 'standard' genetic code

The settings are specified for each run and it's clear it was run two times so far.  Please use this form for all of your protocol sections.

--joe