黑头软口鲦鱼（肥头鲦鱼，Pimephales promelas）基因组的第一代注释。
First-generation annotations for the fathead minnow (Pimephales promelas) genome.
作者信息
Saari Travis W, Schroeder Anthony L, Ankley Gerald T, Villeneuve Daniel L
机构信息
Office of Research and Development, National Health and Environmental Effects Research Laboratory, Mid-Continent Ecology Division, US Environmental Protection Agency, Duluth, Minnesota.
Math, Science, and Technology Department, University of Minnesota Crookston, Crookston, Minnesota, USA.
出版信息
Environ Toxicol Chem. 2017 Dec;36(12):3436-3442. doi: 10.1002/etc.3929. Epub 2017 Aug 29.
Abstract
Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow (Pimephales promelas) genome. We also describe a genome browser, hosted by the Society of Environmental Toxicology and Chemistry, that provides simplified access to the annotation data in context with the genomic sequence. The present study extends the utility of the fathead minnow genome and supports the continued development of this species as a model organism for predictive toxicology. Environ Toxicol Chem 2017;36:3436-3442. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
摘要
从头基因预测和证据比对被用于生成黑头呆鱼（Pimephales promelas）基因组的首批注释。我们还描述了一个由环境毒理学与化学学会托管的基因组浏览器，它能结合基因组序列，为注释数据提供简化的访问途径。本研究扩展了黑头呆鱼基因组的实用性，并支持将该物种持续发展为预测毒理学的模式生物。《环境毒理学与化学》2017年；36:3436 - 3442。2017年由威利期刊公司代表SETAC出版。本文属于美国政府作品，因此在美国处于公共领域。
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2
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Comp Biochem Physiol Part D Genomics Proteomics. 2016 Dec;20:27-40. doi: 10.1016/j.cbd.2016.07.001. Epub 2016 Jul 12.
3
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Sci Data. 2016 May 10;3:160030. doi: 10.1038/sdata.2016.30.
4
A survey of best practices for RNA-seq data analysis.RNA测序数据分析的最佳实践调查。
Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8.
5
Ensembl 2016.Ensembl 2016。
Nucleic Acids Res. 2016 Jan 4;44(D1):D710-6. doi: 10.1093/nar/gkv1157. Epub 2015 Dec 19.
6
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8
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9
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10
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Toxicol Sci. 2012 Dec;130(2):427-39. doi: 10.1093/toxsci/kfs250. Epub 2012 Aug 13.
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