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Molecular building blocks of life in the genomic space

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Gene Catalogs

KEGG GENES is a collection of gene catalogs for all complete genomes (see release history) generated from publicly available resources, mostly NCBI RefSeq and GenBank. They are subject to SSDB computation and KO assignment (gene annotation) by KOALA tool. KEGG DGENES is a supplementary collection of gene catalogs for eukaryotic draft genomes, which are given automatic KO assignment by BlastKOALA with GENES used as a reference data set. KEGG MGENES contains gene catalogs for metagenomes of environmental samples (see also KEGG GENOME) with automatic annotation. The collections of viral genomes and plasmids in RefSeq are now included in KEGG GENES with standard annotation procedures. The organism codes are vg (T40000) and pg (T20000), which may be considered as pan-virus and pan-plasmid codes.
Category Remark
GENES Complete genomes High-quality genomes with KOALA and manual annotations
Plasmids New! Plasmids with KOALA and manual annotations
Viruses New! Viral genomes with KOALA and manual annotations
DGENES Draft genomes Draft genomes with automatic (BlastKOALA) annotation
MGENES Metagenomes Metagenomes with automatic (KAAS) annotation

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Gene Annotation

The annotation of KEGG GENES involves assignment of KO identifiers (K numbers). Internally, this is done using the KOALA and GFIT annotation tools based on the SSDB database (see: Genome Annotation in KEGG). The annotation of KEGG DGENES and MGENES is done automatically using the BlastKOALA and KAAS programs, respectively, shown below.

red Annotate genomes using KEGG GENES
BlastKOALA: automatic KO assignment and pathway/brite/module reconstruction
KAAS: automatic KO assignment and pathway/brite reconstruction
red Search similar sequences in KEGG GENES
BLAST:sequence similarity search by BLAST
FASTA:sequence similarity search by FASTA

Gene Name Conversion

KEGG GENES can be retrieved by giving identifiers of outside databases, such as NCBI-GeneID (Entrez Gene ID), NCBI-gi, and UniProt accession numbers. Cross-reference lists are available at the FTP site.

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Last updated: February 1, 2015
KEGG GenomeNet Kanehisa Laboratories