ftp://ftp.kuicr.kyoto-u.ac.jp/moriya/kaas_sa/index.html

# system require
====================
    perl 5.8 or later (threads Symbol)
    ruby 1.8 or later
    NCBI BLAST (legacy_blast or blast+)
    HMMER 3
    (linux commands; wget, wc, rm, etc.)

# setup
=====================
1. edit kaas.config
    setting for number of CPUs
    path of BLAST and hmmsearch binary files

2. setup the database (or update to latest KEGG GENES and KO)

      % bin/genes_update.pl

# annotate KO to genes
=====================

    % bin/auto_annotate.pl [option] ([orgnism list]) [input]

    input file should be peptide multi-fasta format
    output file
           [input].ko   : gene - ko ID
           [input].oth  : neccessary to reannotation

    option
        -h  : help
        -n  : nucleotide multi-fasta (default : peptide)
        -s  : method based on single-directional best hit
              (default method based on bi-directional best hit)
        -r  : reannotation with KO update without computaton of BLAST
              (counld not change single- or bi-directional method)
        -o  : use old algorithm (ver. 1) (default : ver. 2)
        -p  : use PAM 30 matrix for short sequence (force -s option &
              only ver. 2) (default : BLOSUM 62)

    organism list
         all, rep, erep, brep or path of original organism list file (default : rep)
         rep : representative set for KEGG GENES (./org/org_rep)
         erep : representative set for eukaryotes (./org/org_erep)
         brep : representative set for prokaryotes (./org/org_brep)