Accessing Livestock Resources in Ensembl.
Accessing Livestock Resources in Ensembl.
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访问 Ensebl 中的牲畜资源。
DOI：
10.3389/fgene.2021.650228
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发表时间：
2021
影响因子：
3.7
通讯作者：
Flicek P
中科院分区：
文献类型：
--
作者：
Martin FJ;Gall A;Szpak M;Flicek P
基因组组装比以往任何时候都更便宜、更准确、更自动化。这是由于更具成本效益的化学物质、新的测序技术和更好的算法的结合。牲畜群落一直处于这一基因组组装新浪潮的前沿，产生了一些最高质量的脊椎动物基因组序列。Ensembl的目标是通过我们的基因注释、基因组比对、基因树、调控和变异数据，为这些基因组添加功能和比较注释。我们以高通量和一致的方式运行计算复杂的分析，以帮助加速下游科学。畜牧资源的广度和深度不断扩大。我们为新测序的物种注释参考基因组组合，并定期更新现有基因组的注释。我们是唯一支持品种和其他非参考汇编注释的主要资源。目前，我们提供了13个猪品种的资源，杂交牛的母系和父系单倍型以及各种其他家畜品种的非参考或野生型组合。在这里，我们描述了在Ensembl中存在的牲畜数据，并提供了如何在我们的基因组浏览器中查看数据的协议，通过它下载我们的FTP站点，通过我们的工具操作它，并通过我们的REST API以编程方式与它交互。
Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating some of the highest quality vertebrate genome sequences. Ensembl’s goal is to add functional and comparative annotation to these genomes, through our gene annotation, genomic alignments, gene trees, regulatory, and variation data. We run computationally complex analyses in a high throughput and consistent manner to help accelerate downstream science. Our livestock resources are continuously growing in both breadth and depth. We annotate reference genome assemblies for newly sequenced species and regularly update annotation for existing genomes. We are the only major resource to support the annotation of breeds and other non-reference assemblies. We currently provide resources for 13 pig breeds, maternal and paternal haplotypes for hybrid cattle and various other non-reference or wild type assemblies for livestock species. Here, we describe the livestock data present in Ensembl and provide protocols for how to view data in our genome browser, download via it our FTP site, manipulate it via our tools and interact with it programmatically via our REST API.
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影响因子：
14.9
作者：
Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
通讯作者：
Flicek P
使用多个从头组装全面发现猪基因组中的变异并恢复缺失序列
影响因子：
7
作者：
Li M;Chen L;Tian S;Lin Y;Tang Q;Zhou X;Li D;Yeung CKL;Che T;Jin L;Fu Y;Ma J;Wang X;Jiang A;Lan J;Pan Q;Liu Y;Luo Z;Guo Z;Liu H;Zhu L;Shuai S;Tang G;Zhao J;Jiang Y;Bai L;Zhang S;Mai M;Li C;Wang D;Gu Y;Wang G;Lu H;Li Y;Zhu H;Li Z;Li M;Gladyshev VN;Jiang Z;Zhao S;Wang J;Li R;Li X
通讯作者：
Li X
影响因子：
12.3
作者：
McLaren W;Gil L;Hunt SE;Riat HS;Ritchie GR;Thormann A;Flicek P;Cunningham F
通讯作者：
Cunningham F
影响因子：
14.8
作者：
Kumar, Prateek;Henikoff, Steven;Ng, Pauline C.
通讯作者：
Ng, Pauline C.
DOI：
10.1126/science.1252806
发表时间：
2014-06-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jiang Y;Xie M;Chen W;Talbot R;Maddox JF;Faraut T;Wu C;Muzny DM;Li Y;Zhang W;Stanton JA;Brauning R;Barris WC;Hourlier T;Aken BL;Searle SMJ;Adelson DL;Bian C;Cam GR;Chen Y;Cheng S;DeSilva U;Dixen K;Dong Y;Fan G;Franklin IR;Fu S;Guan R;Highland MA;Holder ME;Huang G;Ingham AB;Jhangiani SN;Kalra D;Kovar CL;Lee SL;Liu W;Liu X;Lu C;Lv T;Mathew T;McWilliam S;Menzies M;Pan S;Robelin D;Servin B;Townley D;Wang W;Wei B;White SN;Yang X;Ye C;Yue Y;Zeng P;Zhou Q;Hansen JB;Kristensen K;Gibbs RA;Flicek P;Warkup CC;Jones HE;Oddy VH;Nicholas FW;McEwan JC;Kijas J;Wang J;Worley KC;Archibald AL;Cockett N;Xu X;Wang W;Dalrymple BP
通讯作者：
Dalrymple BP