KAAS (KEGG Automatic Annotation Server) provides functional annotation of genes in a genome by BLAST comparisons against a manually curated set of ortholog groups in KEGG GENES. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways. This server is used internally to annotate DGENES for draft genomes (4-letter KEGG organism code starting with "d") and EGENES for EST contigs (4-letter KEGG organism codes starting with "e").
Query form
Query sequences
Normally query sequences are amino acid sequences representing a set of protein-coding genes in a complete genome. KO assignments are based on results from BLASTP.
Check the "Nucleotide" checkbox if queries are nucleotide sequences representing a set of EST contigs or ESTs. In this case, KO assignments are based on results from BLASTX and TBLASTN.
In both cases sequences should be in multi-FASTA format.
E-mail address
The URL to access the results will be sent to this address after the assignments are completed.
GENES data set
One or more species may be specified as a template data set for KO assignment.
The computation time taken is proportional to the size of the data set. The accuracy will be improved if closely related species of the query are contained in the data set.
- Representative set (for GENES, for Eukaryotes, for Prokaryotes)
pre-selected data set of species from each taxonomic group in GENES
- Whole set
all KO-assigned species in GENES
- Sub set
any combination of taxonomy group of GENES (one or more of eukaryotes, bacteria or archaea may be selected)
- Manual selection
Template species may be selected using the KEGG organism code excepting codes in DGENES and EGENES.
Assignment method
KO assignment methods may be performed based on the bi-directional best hit (BBH, default) of BLAST or single-directional best hit (SBH).
The computation time of the BBH method is about twice that of SBH. However, the method based on BBH will be more accurate than SBH, if the number of query sequences is large enough (genome scale). If the number of query sequences is small, then the SBH method should suffice (and save time).
Example of result
Users query list
| ID | name | state | start (GMT) | end (GMT) | retry | |
| 1156789000 | Human | computing | 4/01 13:00 2007 | |||
| 1156789012 | E.coli | complete; result | 4/02 7:04 2007 | 4/02 7:15 2007 | ||
| 1156789055 | query070403 | failed | 4/03 12:20 2007 | retry |
'Failed' means abnormal process termination for the trouble with the server or network. You can retry the computation with same file and conditions.
KO list
The flat list of query genes with the K numbers given by the KAAS.
BRITE hierarchies (changed from "KO hierarchy")
The hierarchical list of annotated genes, which is categorized according to the BRITE database.
Pathway map
The list of pathways with linkes to graphical pathway maps.
Reference
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A., and Kanehisa, M.; KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182-W185 (2007). [pubmed] [NAR]
Feedback
Please use the feedback page to send your comments or questions to KAAS.