RiceGAAS: Rice Genome Automated Annotation System
RiceGAAS is a rice genome automated annotation system. This system integrates programs for prediction and analysis of protein-coding gene structure.
Integrated softwares are coding region prediction programs (
FGENESH, MZEF ),
splice site prediction programs (
homology search analysis programs (
tRNA gene prediction program (
repetitive DNA analysis programs (
signal scan search program (
Signal Scan ),
protein localization site prediction program (
PSORT ), and program of
classification and secondary structure prediction of membrane proteins (
Blast against full-length cDNA sequences of japonica rice is integrated. The full-length rice cDNA sequence is provided by KOME database.
Interpretation of the coding region is fully automated and gene prediction is
accomplished without manual evaluation and modification. Therefore some
differences exist between the predicted genes by the system and the manually
predicted genes included in the GenBank entries. Please see "comparison table of gene prediction",
http://RiceGAAS.dna.affrc.go.jp/rga-bin/col_accur.pl in detail.
Further, a unique function is automatically assigned for predicted gene by GFSelector based on the protein homology of the gene.
Additionally, the keyword search from the functions predicted by GFSelector is provided.
|The errors of predicted genes' direction (+/-) in the Location tables were fixed. We are sorry for the inconvenience. Thank you for your cooperation. (2008, Jul 8)|
Browse the annotation results with RiceGAAS and GenBank CDS features for
the rice genome entries in GenBank database
Link from the PAC/BAC clone table sorted by chromosome and clone
name and the keyword search to annotation figures are available.
Automated annotation is re-executed with the latest entries in reference
Predicted genes by the system are shown in "AutoPredgeneset" row on the annotation map. Predicted genes indicateted in the entries in GenBank are shown in "Predgeneset" row on the annotation map.
|Statistics of the predictions||2013 Dec 12|
|No. of PAC/BAC Clones||No. of Bases||No. of Predicted Genes||No. of Predicted Motifs (*1)||No. of predicted LTR Pairs|
|(*1) Predicted by HMMER against Pfam database.|
|Download Rice Genome DataBase File|
Download the rice genome sequences collected from GenBank.
|Guide in filtering the gene models.|
This page provides a guide in filtering the predicted gene models such as filtering out gene models in non-Nipponbare BAC/PAC sequences and duplicated gene models in overlapping regions between clones.
|This page is the entry for web service of RiceGAAS. The system supports computational analyses of your query genomic sequence and graphical result view. In order to use this service, you must register your e-mail address and password. This procedure is necessary to protect your data from the third party.|
|RiceCpGViewer shows the distribution of CpG dinucleotides together with the positions of exons of each predicted gene along rice chromosomes.|
The development of this system was supported by a grant from
the Ministry of Agriculture, Forestry and Fisheries of Japan
(Rice Genome Project SY1101, SY1103, GS-1302).
Users are asked to cite this URL (http://RiceGAAS.dna.affrc.go.jp/) or the
following article when publishing results, which have been obtained with the
system described here. Reference: Sakata,K., Nagamura,Y., Numa,H.,
Antonio,B.A., Nagasaki,H., Idonuma,A., Watanabe,W., Shimizu,Y., Horiuchi,I.,
Matsumoto,T., Sasaki,T. & Higo,K.:
"RiceGAAS: an automated annotation system and database for rice genome sequence"
, Nucleic Acids Res., 30: 98-102
For the detailed algorithm and applications, please refer to JARQ 43 (2), 103 - 113 (2009).
We welcome comments and suggestions on the system.
Send questions on server/software trouble to support staff at firstname.lastname@example.org.
Tutorial for rice genome database:
Sep 16, 2008