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The Genome Sequence DataBase

C. Harger
2000 Nucleic Acids Research  
The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information.  ...  The content of GSDB remains up-to-date because publicly available data is acquired from the International Nucleotide Sequence Database Collaboration databases (IC) on a nightly basis.  ...  INTRODUCTION The Genome Sequence DataBase (GSDB), operated by the National Center for Genome Resources (NCGR), is a relational database of publicly available nucleotide sequences and associated biological  ... 
doi:10.1093/nar/28.1.31 pmid:10592174 pmcid:PMC102463 fatcat:2igvanrohbd6xbeicalhl7c65a

The Sequenced Angiosperm Genomes and Genome Databases

Fei Chen, Wei Dong, Jiawei Zhang, Xinyue Guo, Junhao Chen, Zhengjia Wang, Zhenguo Lin, Haibao Tang, Liangsheng Zhang
2018 Frontiers in Plant Science  
Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing.  ...  Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including  ...  ACKNOWLEDGMENTS This work was supported by the National Key Research and Development Program of China (2016YFD0100305) and National Natural Science Foundation of China (81502437), and a start-up fund from  ... 
doi:10.3389/fpls.2018.00418 pmid:29706973 pmcid:PMC5909171 fatcat:v5av6eiadrgw5lmt2qmzqlesrq

The Genome Sequence DataBase (GSDB): meeting the challenge of genomic sequencing

G Keen
1996 Nucleic Acids Research  
The genome sequence database (GSDB) is a complete, publicly available relational database of DNA sequences and annotation maintained by the National Center for Genome Resources (NCGR) under a Cooperative  ...  GSDB provides direct, client-server access to the database for data contributions, community annotation and SQL queries.  ...  ACKNOWLEDGEMENTS The Genome Sequence DataBase is supported by Cooperative Agreement 95ER62062 between the National Center for Genome Resources and the US Department of Energy, Office of Health and Environmental  ... 
doi:10.1093/nar/24.1.13 pmid:8594561 pmcid:PMC145611 fatcat:4ryuhvekv5gm3ectcxxhhqdxoi

INE: The Rice Genome Sequence Database

Yoshiyuki Mukai, Hideki Nagasaki, Baltazar A. Antonio, Katsumi Sakata, Yasumichi Sakai, Takuji Sasaki
1999 Genome Informatics Series  
Acknowledgment This work is supported by the Ministry of Agriculture , Forestry and Fisheries (MAFF) and the Japan Racing Association (JRA). The MAFF DNA Bank provides the server for INE .  ...  So far sequenced PACs with the completed annotation are already incorporated in this database. As the different groups accumulate genome sequence, the data will be deposited in this database.  ...  :82/giot/INE.html) to serve as the central data resource for the rice genome sequencing effort. 2 Features of INE Database INE is primarily designed to integrate all the genome information in rice.  ... 
doi:10.11234/gi1990.10.276 fatcat:y66bk4ieazgrvczi33j6d2wxvu

Sequence resources at the Candida Genome Database

M. B. Arnaud, M. C. Costanzo, M. S. Skrzypek, P. Shah, G. Binkley, C. Lane, S. R. Miyasato, G. Sherlock
2007 Nucleic Acids Research  
In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD  ...  The Candida Genome Database (CGD, http://www. candidagenome.org/) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology  ...  and reconcile versions of the sequence; and Mike Cherry and the SGD Group for helpful advice and discussions.  ... 
doi:10.1093/nar/gkl899 pmid:17090582 pmcid:PMC1669745 fatcat:wr5gl2rnvbfqta6duvzamgh7ou

The Genome Sequence DataBase: towards an integrated functional genomics resource

M. P. Skupski, M. Booker, A. Farmer, M. Harpold, W. Huang, J. Inman, D. Kiphart, C. Kodira, S. Root, F. Schilkey, J. Schwertfeger, A. Siepel (+6 others)
1999 Nucleic Acids Research  
During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data  ...  The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within  ...  ACKNOWLEDGEMENTS This work was funded by Cooperative Agreement DE-FC03-95ER62062 with the Office of Biological and Environmental Research of the Department of Energy.  ... 
doi:10.1093/nar/27.1.35 pmid:9847136 pmcid:PMC148091 fatcat:22zl4wfdfrd37nbj23zssjx4gm

Drosophila Genomic Sequence Annotation Using the BLOCKS+ Database

J. G. Henikoff
2000 Genome Research  
Detecting a hit in a sequence data bank is frequently the best clue as to the function of a gene, so that sequence similarity searching is de rigeur for any genomic annotation effort.  ...  Each strand of the entire sequence was used as query of the BLOCKS+ database of conserved regions of proteins.  ...  ACKNOWLEDGMENTS We thank the GASP team for motivating this study. This work was supported by a grant from NIH. The publication costs of this article were defrayed in part by payment of page charges.  ... 
doi:10.1101/gr.10.4.543 pmid:10779495 pmcid:PMC310867 fatcat:wfdq6bhrkrcj7acyzaobfvjlai

The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes

C. Harger, M. Skupski, E. Allen, C. Clark, D. Crowley, E. Dickinson, D. Easley, A. Espinosa-Lujan, A. Farmer, C. Fields, L. Flores, L. Harris (+23 others)
1997 Nucleic Acids Research  
The Genome Sequence DataBase (GSDB) has completed its conversion to an improved relational database. The new database, GSDB 1.0, is fully operational and publicly available.  ...  All methods of data contribution and data retrieval fully support the new data types that have been incorporated into GSDB, including discontiguous sequences, multiple sequence alignments, and community  ...  ACKNOWLEDGMENTS The Genome Sequence DataBase is supported by Cooperative Agreement DE-FC03-95ER62062 between the National Center for Genome Resources and the US Department of Energy, Office of Health and  ... 
doi:10.1093/nar/25.1.18 pmid:9016496 pmcid:PMC146367 fatcat:gzsalve45fedjhxzu4hsxa4ali

Protein sequence databases in the context of genome projects

Amos Bairoch
1994 Genome Informatics Series  
Recent developments concerning the SWISS-PROT and PROSITE databases are discussed in the context of genome projects and of new network access tools SWISS-PROT[1] is a curated protein sequence database  ...  In the recent months we have developed the database in the following directions: • We have selected a number of organisms that are the target of genome sequencing and/or mapping projects and for which  ...  PROSITE [2] is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences  ... 
doi:10.11234/gi1990.5.238 fatcat:si2f7vc5nzbplddrcl5n4jr7sa

Beyond the human genome sequencing. HOWDY: An integrated human genome database

Mika HIRAKAWA, Katsuji MATSUMURA, Masako KURODA
2001 Journal of Information Processing and Management  
Author Abstract: More than 90 percent of the whole human genomic DNA that includes 3 billion bases has sequenced and published by the Human Genome Project over past 10 years.  ...  As a part of ALIS (Advanced Science Information Systems) Project, we have developed a database named HOWDY that can link many different human genome databases on the Internet dynamically.  ...  1 科学技術振興事業団 データベース開発部(〒102-8666 東京都千代田区四番町5-3) Tel. 03(5214)8491 E-mail: mhirakaw@jst.go.jp 1 Japan Science and Technology Corporation, Advanced Databases Department (5-3, Yonban-cho, Chiyoda-ku  ... 
doi:10.1241/johokanri.44.342 fatcat:cwyleefthzechgljbjc7txt36m

gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

So Nakagawa, Mahoko Ueda Takahashi
2016 Database: The Journal of Biological Databases and Curation  
The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes.  ...  In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian  ...  Computations were performed partially on the NIG supercomputer at the ROIS National Institute of Genetics.  ... 
doi:10.1093/database/baw087 pmid:27242033 pmcid:PMC4885607 fatcat:vw27iroitbhdjnmew3ez46ajke

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

A. J. Cox, M. J. Bauer, T. Jakobi, G. Rosone
2012 Bioinformatics  
With these techniques, a 45x coverage of real human genome sequence data compresses losslessly to under 0.5 bits per base, allowing the 135.3Gbp of sequence to fit into only 8.2Gbytes of space (trimming  ...  these techniques from being widely applied to the large sets of sequences often encountered as the outcome of DNA sequencing experiments.  ...  ACKNOWLEDGEMENT The authors would like to thank Dirk Evers for his support throughout this project.  ... 
doi:10.1093/bioinformatics/bts173 pmid:22556365 fatcat:fz2icliuazaifkskeyvvzgbmce

ChickVD: a sequence variation database for the chicken genome

J. Wang
2004 Nucleic Acids Research  
We compared the sequence reads from the three chicken breeds to the 6.6X RJF reference genome sequence (Chicken Genome Consortium, 2004).  ...  University Genome Sequencing Center (WUGSC), as a reference chicken genome sequence (Chicken Genome Consortium, 2004).  ... 
doi:10.1093/nar/gki092 pmid:15608233 pmcid:PMC540046 fatcat:u6bdm6ialbbdxcigzohb2qvxtm

SSRD: Simple Sequence Repeats Database of the Human Genome

Subbaya Subramanian, Vamsi M. Madgula, Ranjan George, Satish Kumar, Madhusudhan W. Pandit, Lalji Singh
2003 Comparative and Functional Genomics  
The simple sequence repeats database (SSRD) for the human genome was created for easy access to such repeats, for analysis, and to be used to understand their biological significance.  ...  The resource will facilitate repeat sequence analysis in the human genome and the understanding of the functional and evolutionary significance of simple sequence repeats.  ...  Acknowledgements The authors would like to thank Sreedhar, Kavitha, Siva Prasad and Saritha for their support in developing the SSRD database.  ... 
doi:10.1002/cfg.289 pmid:18629286 pmcid:PMC2448451 fatcat:soqjbcwkinhhpalpeedafdk2pa

The Genbank Database and the Flow of Sequence Data for the Human Genome [chapter]

Christian Burks
1988 Biotechnology and the Human Genome  
Therefore, if one goal of sequencing a complete genome is to get a picture of the information set necessary rough calculation, in GenBank there is about 20% of the complete genome, and this is the  ...  That allows one to lump from our database into the human gene mapping library database in New Haven using the human gene names to link those sequences-thus connecting genes that have been sequenced with  ... 
doi:10.1007/978-1-4684-5547-2_6 fatcat:ajm35ntehbar7jgph7ncxp5ab4
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