KEGG Organisms
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KEGG GENES is a collection of gene catalogs for all complete genomes generated from publicly available resources, mostly NCBI RefSeq.
They are subject to SSDB computation and manual KO assignment (gene annotation).
KEGG DGENES for draft genomes of some eukaryotes and KEGG EGENES for EST datasets of mostly plants are supplementary gene catalogs, which are given automatic KO assignment with GENES used as a reference data set.
The organisms in GENES, DGENES, and EGENES constitute KEGG GENOME, or the KEGG organisms identified by the three-letter KEGG organism codes (with prefix "d" for draft genomes and "e" for EST contigs).
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Gene Annotation
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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: Ortholog Annotation in KEGG).
The annotation of KEGG DGENES and EGENES is done automatically using the KAAS program, and EGENES is generated from EST datasets by the EGassembler program. Both of these programs are made publicly available.
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 Annotate genomes using KEGG
KAAS: automatic annotation (KO assignment) and pathway reconstruction
[reference]
Generate EST consensus contigs
EGassembler: automatic assembly of ESTs to generate consensus contigs
[reference]
Search similar sequences in GENES
| BLAST: | sequence similarity search by BLAST |
| FASTA: | sequence similarity search by FASTA |
Gene Name Conversion
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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: October 5, 2009
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