On 13 Aug 2002 15:14:08 -0300, Henry Lenzi wrote: > 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 Hi. The manual for the development version of ACT has a little bit more information about using MSPcrunch: http://www.sanger.ac.uk/Software/ACT/current_manual/start.html#COMPARISON-RUN However we now recommend using the development version of ACT and blastall version 2.2.2. ACT can read blast v2.2.2 output so you can avoid having to run MSPcrunch. For your example above you should try something like this with v2.2.2: blastall -m 8 -t brucei.fasta -d tcruzi.fasta -p tblastx -o myblast1.out Please contact me if you have any questions about this. > What are the annotated (embl) files for? The EMBL files are needed so that you can see the annotated features in ACT, rather than just the raw sequence. Kim.
