[artemis-users] Questions regarding ACT - what do you do after you MSPcrunch thedata?

[Henry Lenzi]

Hello --

        I've read a tutorial on ACT that says you need to have, e.g.,

        tbrucei.fasta
        tcruzi.fasta
        tbrucei.embl
        tcruzi.embl

        Then it says you have to process the fasta files by formating the files
with 

$formatdb -i t.cruzii -p F

then blastall

$blastall -t brucei.fasta -d tcruzi.fasta -p tblastx -o myblast1.out

And finally, MSPcrunch them:

$MSPcrunch -d -I50 myblast.out > myblast.crunch


        What are the annotated (embl) files for?

        I feel that the chapter on the tutorial explaining how to make a
comparison file is way too short. This should be very thoroughly
explained since it a crucial step...

        Thank you,

        Henry