RiceGAAS: an automated annotation system and database for rice genome sequence

Abstract

An extensive effort of the International Rice Genome Sequencing Project (IRGSP) has resulted in rapid accumulation of genome sequence, and >137 Mb has already been made available to the public domain as of August 2001. This requires a high-throughput annotation scheme to extract biologically useful and timely information from the sequence data on a regular basis. A new automated annotation system and database called Rice Genome Automated Annotation System (RiceGAAS) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation. The system has the following functional features: (i) collection of rice genome sequences from GenBank; (ii) execution of gene prediction and homology search programs; (iii) integration of results from various analyses and automatic interpretation of coding regions; (iv) re-execution of analysis, integration and automatic interpretation with the latest entries in reference databases; (v) integrated visualization of the stored data using web-based graphical view. RiceGAAS also has a data submission mechanism that allows public users to perform fully automated annotation of their own sequences. The system can be accessed at http://RiceGAAS.dna.affrc.go.jp/.

Two Adjacent Nucleotide-Binding Site–Leucine-Rich Repeat Class Genes Are Required to Confer Pikm-Specific Rice Blast Resistance

“…Sequence annotation and computational analysis of DNA: The Rice Genome Automated Annotation System (RiceGAAS) (Sakata et al 2002) was used to analyze genomic sequence data. This system integrates the programs GENSCAN, RiceHMM, FGENESH, and MZEF for finding putative gene regions and the homology-search-analysis programs Blast, HMMER, ProfileScan, and MOTIF for predicting the putative functions of genes.…”

Structural and Transcriptional Analysis of the Self-Incompatibility Locus of Almond: Identification of a Pollen-Expressed F-Box Gene with Haplotype-Specific Polymorphism

“…A total of ‫ف‬ 1000 sequences, which included PCR products filling gaps between the shotgun contigs, were assembled and gave a nucleotide sequence of 71,953 bp. The ‫ف‬ 70-kb sequence was annotated by RiceGAAS (Rice Genome Automated Annotation System [Sakata et al, 2002]; http://ricegaas. dna.affrc.go.jp/index.html), which automatically analyzes large sequences using several programs for the prediction and analysis of protein-coding sequences: BLAST (Basic Local Alignment Search Tool [Altschul et al, 1990]), AutoPredLTR (Sakata et al, 2002), and GENSCAN (Burge and Karlin, 1997).…”

“…NP79R sequence has been shown to be conserved in different S haplotypes of almond (Ushijima et al, 2001 (A) Scheme of the S c haplotype-specific region. The nucleotide sequence of the ‫-07ف‬kb S c haplotype-specific region was characterized by GEN-SCAN, BLASTX, and AutoPredLTR search of RiceGAAS (Sakata et al, 2002). The A nucleotide of the putative initiation codon (ATG) of the S c -RNase gene (Ushijima et al, 1998) is positioned as ϩ1.…”

Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat[W]

“…Two hypothetical genes ( TmHG-1 and TmHG-2 ) were predicted by the RiceGAAS annotation system (Sakata et al, 2002), and corresponding ESTs were found (see supplemental data online). Close to the right end of the contig and upstream of TmSTF-1 , two pseudogenes were found: TmRGL-1 belongs to the NBS-LRR resistance gene analog type, and TmPIK-1 shows similarity to a phosphatidylinositol-3 kinase gene from soybean.…”

“…Direct and inverted repeat sequences were identified with the GCG program BESTFIT and dot-plot analysis of the query sequence against itself. For gene prediction in regions in which no putative genes or repetitive elements were identified by BLASTX or BLASTN, the RiceGAAS annotation system (Sakata et al, 2002) was used. Predicted genes were considered if they were predicted by at least two prediction programs.…”