Databases and Information Integration for the Medicago truncatula Genome and Transcriptome
Author:
Cannon Steven B.1, Crow John A.1, Heuer Michael L.1, Wang Xiaohong1, Cannon Ethalinda K.S.1, Dwan Christopher1, Lamblin Anne-Francoise1, Vasdewani Jayprakash1, Mudge Joann1, Cook Andrew1, Gish John1, Cheung Foo1, Kenton Steve1, Kunau Timothy M.1, Brown Douglas1, May Gregory D.1, Kim Dongjin1, Cook Douglas R.1, Roe Bruce A.1, Town Chris D.1, Young Nevin D.1, Retzel Ernest F.1
Affiliation:
1. Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (S.B.C., X.W., E.K.S.C., J.V., J.M., N.D.Y.); Center for Computational Genomics and Bioinformatics, University of Minnesota, Minneapolis, Minnesota 55455 (J.A.C., M.L.H., C.D., A.F.L., T.M.K., E.F.R.); Department of Plant Pathology, University of California, Davis, California 95616 (A.C., J.G., D.J.K., D.R.C.); The
Abstract
Abstract
An international consortium is sequencing the euchromatic genespace of Medicago truncatula. Extensive bioinformatic and database resources support the marker-anchored bacterial artificial chromosome (BAC) sequencing strategy. Existing physical and genetic maps and deep BAC-end sequencing help to guide the sequencing effort, while EST databases provide essential resources for genome annotation as well as transcriptome characterization and microarray design. Finished BAC sequences are joined into overlapping sequence assemblies and undergo an automated annotation process that integrates ab initio predictions with EST, protein, and other recognizable features. Because of the sequencing project's international and collaborative nature, data production, storage, and visualization tools are broadly distributed. This paper describes databases and Web resources for the project, which provide support for physical and genetic maps, genome sequence assembly, gene prediction, and integration of EST data. A central project Web site at medicago.org/genome provides access to genome viewers and other resources project-wide, including an Ensembl implementation at medicago.org, physical map and marker resources at mtgenome.ucdavis.edu, and genome viewers at the University of Oklahoma (www.genome.ou.edu), the Institute for Genomic Research (www.tigr.org), and Munich Information for Protein Sequences Center (mips.gsf.de).
Publisher
Oxford University Press (OUP)
Subject
Plant Science,Genetics,Physiology
Reference34 articles.
1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25
: 3389–3402 2. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, et al (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32
: D115–D119 3. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9
: 208–218 4. Bell CJ, Dixon RA, Farmer AD, Flores R, Inman J, Gonzales RA, Harrison MJ, Paiva NL, Scott AD, Weller JW, et al (2001) The Medicago Genome Initiative: a model legume database. Nucleic Acids Res 29
: 114–117 5. Birney E, Andrews D, Bevan P, Caccamo M, Cameron G, Chen Y, Clarke L, Coates G, Cox T, Cuff J, et al (2004) An overview of Ensembl. Nucleic Acids Res 32
: D468–D470
Cited by
55 articles.
订阅此论文施引文献
订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献
|
|