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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

Bioinformatics issues for automating the annotation of genomic sequences

by Kim Carter Akira Oka, Gen Tamiya Matthew I. Bellgard - Genome Informatics , 2001
"... The rapid explosion in the amount of biological data being generated worldwide is surpassing efforts to manage analysis of the data. As part of an ongoing project to automate and manage bioinformatics analysis, the authors have designed and implemented a simple automated annotation system, which is ..."
Abstract - Cited by 4 (0 self) - Add to MetaCart
important issues that need to be addressed in order to automate the re-analysis/re-annotation of genomic sequences within a reasonable timeframe.

A Multi-Agent System for Automated Genomic Annotation

by Keith Decker, Xiaojing Zheng - In Proceedings of the 5th Intl. Conf. on Autonomous Agents , 2001
"... Massive amounts of raw data are currently being generated by biologists while sequencing organisms. Outside of the largest, high-profile projects such as the Human Genome Project, most of this raw data must be analyzed through the piecemeal application of various computer programs and searches of va ..."
Abstract - Cited by 14 (3 self) - Add to MetaCart
state of the art. We have used DECAF, a multi-agent system toolkit based on RETSINA and TAEMS, to construct a prototype multi-agent system for automated annotation and database storage of sequencing data for herpes viruses. The resulting system eliminates tedious and always out-of-date hand analyses

KAIKOGAAS: An Automated Annotation System for Silkworm

by Michihiko Shimomura, Yuji Shimizu, Baltazar A. Antonio, Yoshiaki Nagamura, Kazuei Mita, Takuji Sasaki
"... The Silkworm Genome Research Program (SGP) has completed a threefold draft sequence of the silkworm (Bombyx mori) genome by shotgun sequencing thereby establishing a basic resource for comprehensive structural and functional analysis [1]. An annotation tool and database called KAIKOGAAS (Kaiko Genom ..."
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The Silkworm Genome Research Program (SGP) has completed a threefold draft sequence of the silkworm (Bombyx mori) genome by shotgun sequencing thereby establishing a basic resource for comprehensive structural and functional analysis [1]. An annotation tool and database called KAIKOGAAS (Kaiko

Evaluation of three automated genome annotations for Halorhabdus utahensis

by Peter Bakke, Nick Carney, Will Deloache, Mary Gearing, Kjeld Ingvorsen, Matt Lotz, Jay Mcnair, Pallavi Penumetcha, Samantha Simpson, Laura Voss, Max Win, Laurie J. Heyer, A. Malcolm - PLoS ONE , 2009
"... Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited in databa ..."
Abstract - Cited by 9 (0 self) - Add to MetaCart
Genome annotations are accumulating rapidly and depend heavily on automated annotation systems. Many genome centers offer annotation systems but no one has compared their output in a systematic way to determine accuracy and inherent errors. Errors in the annotations are routinely deposited

BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res

by Gary H. Van Domselaar, Paul Stothard, Savita Shrivastava, Joseph A. Cruz, Anchi Guo, Xiaoli Dong, Paul Lu, Duane Szafron, Russ Greiner, David S. Wishart , 2005
"... BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and hyper-link ..."
Abstract - Cited by 67 (5 self) - Add to MetaCart
BASys (Bacterial Annotation System) is a web server that supports automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. It accepts raw DNA sequence data and an optional list of gene identification information and provides extensive textual annotation and hyper

KOBAS server: a web-based platform for automated annotation and pathway identification

by Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, Liping Wei - Nucleic Acids Res , 2006
"... There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experi-ments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously demon ..."
Abstract - Cited by 54 (7 self) - Add to MetaCart
There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experi-ments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously

AGeS: A Software System for Microbial Genome Sequence Annotation

by Kamal Kumar, Valmik Desai, Li Cheng, Maxim Khitrov, Deepak Grover, Ravi Vijaya Satya, Chenggang Yu, Nela Zavaljevski, Jaques Reifman
"... Background: The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate ..."
Abstract - Cited by 4 (1 self) - Add to MetaCart
Background: The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need

Small RNA in rice genome

by Wang Kai, Zhu Xiaopeng, Zhong Lan, Chen Runsheng , 2002
"... Abstract Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice ge-nome finishin ..."
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finishing map, the next urgent step for rice researchers is to annotate the genes and non-coding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play signifi-cant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other

Small Genome Annotation and Data Management at TIGR

by Michelle Gwinn, William Nelson, Robert Dodson, Steven Salzberg, Owen White
"... TIGR has developed, and continues to refine, a comprehensive, efficient system for small genome annotation. The Glimmer gene finding software identifies open reading frames most likely to code for genes. The protein sequences from these genes are searched against a nonredundant protein database, pro ..."
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TIGR has developed, and continues to refine, a comprehensive, efficient system for small genome annotation. The Glimmer gene finding software identifies open reading frames most likely to code for genes. The protein sequences from these genes are searched against a nonredundant protein database
Results 1 - 10 of 31