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README for the "genes" subdirectory
===================================

Genome annotation in KEGG is a process to make links between genes
in the complete genomes to molecules in the molecular networks.
This is represented mainly by the following three databases:

   KEGG ORTHOLOGY (KO) - consists of KEGG Orthology (KO) entries
      representing functional orthologs that generally correspond to
      KEGG pathway nodes and BRITE hierarchy nodes 
   KEGG GENES - a collection of gene catalogs for all complete genomes
      (KEGG organisms) generated mostly from NCBI RefSeq and GenBank,
      supplemented by the viruses and addendum categories
   KEGG GENOME - contains organism-level information about complete
      genomes

This directory contains the following files

   ko.tar.gz                  - KO entries
   genome.tar.gz              - genome entries
   organisms/org/             - annotated gene catalogs of KEGG organism
     org/Tnum.ent.gz          - entry file
     org/Tnum.pep.gz          - amino acid sequence file
     org/Tnum.nuc.gz          - nucleotide sequence file
     org/Tnum.genome.gz       - genome sequence file
     org/Tnum.kff.gz          - KEGG feature format file
     org/org_link.tar.gz      - link information files
   organisms_new/org/         - unannotated gene catalogs of KEGG organisms
   viruses/                   - gene set of all viruses
   addendum/                  - gene set of addendum category
   fasta/                     - fasta sequence files and auxiliary files
                                (see separate README file)
   oc/oc.gz                   - Ortholog Clusters (OC) computationally
                                generated from KEGG SSDB
   misc/                      - miscellaneous files for taxonomy, etc.
   links/                     - ID mapping files of GENES to/from KO, PATHWAY,
                                MODULE, NCBI-GeneID, NCBI-ProteinID and UniProt

where "org" is the three- or four-letter organism code and "Tnum" is the
T number identifier.

The T numbers and the two-letter codes for "viruses" and "addendum" are:
T40000 (vg) and T10000 (ag), respectively. The "viruses" and "addendum"
subdirectories additionally contains T40000.tax.gz and T10000.tax.gz for
NCBI taxonomy IDs.

The contents of tarballs are as follows.

ko.tar.gz
---------
  ko                 - DBGET flat file containing all KO entries
  ko_dbname.list     - ID mapping files of KO to/from other KEGG DBs,
                       PubMed, COG, GO, CAZy and TC

genome.tar.gz
-------------
  genome             - DBGET flat file containing all GENOME entries
  genome_dbname.list - ID mapping files of GENOME to/from other KEGG DBs,
                       PubMed, RefSeq, GenBank, Assembly and Taxonomy

org_link.tar.gz
---------------
  org_dbname.list    - ID mapping files of KEGG organisms to/from other
                       KEGG DBs, NCBI-GeneID, NCBI-ProteinID, OMIM, UniProt,
                       and many other databases

The .kff file contains the following information for each gene in the genome:

   column 1  - KEGG GENES identifier (in the form of org:gene)
   column 2  - Feature key such as CDS, tRNA, rRNA, ncRNA, lncRNA, miRNA, and
               gene (usually meaning pseudogene)
   column 3  - Amino acid sequence length
   column 4  - Nucleotide sequence length
   column 5  - Geonomic position
   column 6  - NCBI GeneID
   column 7  - NCBI ProteinID
   column 8  - Gene name
   column 9  - Definition in the original DB
   column 10 - KO identifier (K number)
   column 11 - KO definition

All the amino acid sequence file (Tnum.pep.gz) in KEGG GENES are concatenated
into a single file and stored in the fasta directory. Some of the outside
links (org_link.tar.gz) for all organisms in KEGG GENES are also duplicated
in the links directory.

KEGG SSDB (not distributed) is a huge database containing similarity
scores computed by SSEARCH and best hit relations determined for all
genome pairs in KEGG GENES. This information is used in the KOALA (KEGG
Orthology and Links Annotation) tool to perform, both computationally
and manually, cross-species annotation (K number assignment) of KEGG
GENES.

KEGG OC is an auxiliary dataset containing ortholog clusters
computationally generated by a program to search quasi-cliques in
the SSDB graph.


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Updated: June 14, 2017

(c) Kanehisa Laboratories