Results 1 - 10 of 47

Rice Annotation Database (RAD): a contig-oriented

by Yuichi Ito, Kohji Arikawa, Baltazar A. Antonio, Isamu Ohta, Shinji Naito, Yoshiyuki Mukai, Atsuko Shimano, Masatoshi Masukawa, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Junri Yokoyama, Yasumichi Sakai, Katsumi Sakata, Yoshiaki Nagamura, Nobukazu Namiki, Takashi Matsumoto, Kenichi Higo, Takuji Sasaki , 2004
"... database for map-based rice genomics ..."
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database for map-based rice genomics

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics

by Hiroaki Sakai, Sung Shin Lee, Tsuyoshi Tanaka, Hisataka Numa, Jungsok Kim, Yoshihiro Kawahara, Akira Muto, Hachiro Inokuchi, Toshimichi Ikemura, Takashi Matsumoto, Takuji Sasaki, Takeshi Itoh - Plant Cell Physiol , 2013
"... rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest ..."
Abstract - Cited by 36 (3 self) - Add to MetaCart
newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations

The Institute for Genomic Research Osa1 rice genome annotation database

by Qiaoping Yuan , Shu Ouyang , Aihui Wang , Wei Zhu , Rama Maiti , Haining Lin , John Hamilton , Brian Haas , Razvan Sultana , Foo Cheung , Jennifer Wortman , C Robin Buell - Plant Physiol , 2005
"... We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virt ..."
Abstract - Cited by 50 (6 self) - Add to MetaCart
We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules

rice genome

by Nikoleta Juretic, Thomas E. Bureau, Richard M. Bruskiewich , 2003
"... Motivation: The high content of repetitive sequences in the genomes of many higher eukaryotes renders the task of annotating them computationally intensive. Presently, the only widely accepted method of searching and annotating transposable elements (TEs) in large genomic sequences is the use of the ..."
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applied to known model TE families in genomic DNA. Results: We used a combination of computational approaches to annotate the TEs in the finished genome of Oryza sativa ssp. japonica. In this paper, we discuss the strengths and the weaknesses of the annotation methods used. These approaches included

Genome Informatics 13: 521–522 (2002) 521 RAD: Rice Annotation Database

by Takuji Sasaki
"... The Rice Genome Research Program (RGP) has been pursuing the sequencing of the entire genome ..."
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The Rice Genome Research Program (RGP) has been pursuing the sequencing of the entire genome

DATABASE Open Access Rice-Map: a new-generation rice genome browser

by Jun Wang, Lei Kong, Shuqi Zhao, He Zhang, Liang Tang, Zhe Li, Xiaocheng Gu, Jingchu Luo, Ge Gao
"... Background: The concurrent release of rice genome sequences for two subspecies (Oryza sativa L. ssp. japonica and Oryza sativa L. ssp. indica) facilitates rice studies at the whole genome level. Since the advent of highthroughput analysis, huge amounts of functional genomics data have been delivered ..."
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delivered rapidly, making an integrated online genome browser indispensable for scientists to visualize and analyze these data. Based on next-generation web technologies and high-throughput experimental data, we have developed Rice-Map, a novel genome browser for researchers to navigate, analyze

The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res

by Hajime Ohyanagi, Tsuyoshi Tanaka, Hiroaki Sakai, Yasumasa Shigemoto, Kaori Yamaguchi, Takuya Habara, Yasuyuki Fujii, Baltazar A. Antonio, Yoshiaki Nagamura, Tadashi Imanishi, Kazuho Ikeo, Takeshi Itoh, Takashi Gojobori, Takuji Sasaki , 2006
"... With the completion of the rice genome sequencing, a standardized annotation is necessary so that the 20 information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating and man ..."
Abstract - Cited by 39 (4 self) - Add to MetaCart
With the completion of the rice genome sequencing, a standardized annotation is necessary so that the 20 information from the genome sequence can be fully utilized in understanding the biology of rice and other cereal crops. An annotation jamboree was held in Japan with the aim of annotating

RetrOryza: a database of the rice LTR-retrotransposons

by Cristian Chaparro, Romain Guyot, Andrea Zuccolo, Olivier Panaud - Nucleic Acids Res , 2007
"... Long terminal repeat (LTR)-retrotransposons com-prise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influ-ence the expression of neighboring genes, the co ..."
Abstract - Cited by 4 (0 self) - Add to MetaCart
Long terminal repeat (LTR)-retrotransposons com-prise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influ-ence the expression of neighboring genes

DATABASE Open Access OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics

by Mohamed Helmy, Masaru Tomita, Yasushi Ishihama
"... Background: Proteogenomics aims to utilize experimental proteome information for refinement of genome annotation. Since mass spectrometry-based shotgun proteomics approaches provide large-scale peptide sequencing data with high throughput, a data repository for shotgun proteogenomics would represent ..."
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represent a valuable source of gene expression evidence at the translational level for genome re-annotation. Description: Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version

DATABASE Open Access PRIN: a predicted rice interactome network

by Haibin Gu, Pengcheng Zhu, Yinming Jiao, Yijun Meng, Ming Chen
"... Background: Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. Although high-throughput technologies such as yeast two-hybrid system and affinity purification followed ..."
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are also mapped to our network for validation. Finally, a user-friendly web interface was developed to offer convenient database search and network visualization. Conclusions: PRIN is the first well annotated protein interaction database for the important model plant Oryza sativa. It has greatly extended
Results 1 - 10 of 47