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 ( GENSCAN, RiceHMM, FGENESH, MZEF ), splice site prediction programs ( SplicePredictor ), homology search analysis programs ( Blast, HMMER, ProfileScan, MOTIF ), tRNA gene prediction program ( tRNAscan-SE ), repetitive DNA analysis programs ( RepeatMasker, Printrepeats ), signal scan search program ( Signal Scan ), protein localization site prediction program ( PSORT ), and program of classification and secondary structure prediction of membrane proteins ( SOSUI ).

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.

  • Bug fixing

    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)

  • Rice Genome Annotation Database

    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 databases.
    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 2015 Sep 3
    No. of PAC/BAC Clones No. of Bases No. of Predicted Genes No. of Predicted Motifs (*1) No. of predicted LTR Pairs
    4,667 618,539,485 146,765 164,217 7,280
    (*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.

  • Analyses for Your Genomic Sequences

    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

    RiceCpGViewer shows the distribution of CpG dinucleotides together with the positions of exons of each predicted gene along rice chromosomes.

    Reference to RiceGAAS:
    Contact us:

    System flowchart:

    Tutorial for rice genome database:

    Server access logs:

    Sep 16, 2008