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The Ensembl gene annotation system

Bronwen L. Aken, Sarah Ayling, Daniel Barrell, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, Konstantinos Billis, Carlos García Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri (+12 others)
<span title="">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects.  ...  Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets.  ...  We thank the members of the Ensembl project, past and present, for their support and Guy Coates, Peter Clapham and Tim Cutts for maintaining the Ensembl computer systems. Conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw093">doi:10.1093/database/baw093</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27337980">pmid:27337980</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4919035/">pmcid:PMC4919035</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jsnympsq4rczzhh5nupzv5b4ha">fatcat:jsnympsq4rczzhh5nupzv5b4ha</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720175927/http://uu.diva-portal.org/smash/get/diva2:1034550/FULLTEXT01" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e3/5c/e35cd6eec3ccd1d1b273d837147b2ba0fbccaeab.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baw093"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919035" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Ensembl Automatic Gene Annotation System

V. Curwen
<span title="2004-05-01">2004</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
We also thank the zebrafish informatics group at the Sanger Institute, and in particular Kerstin Jekosch, for their feedback on the gene build system.  ...  We particularly acknowledge the Singapore members of the Fugu annotation project, the finished analysis group, and the annotation team at the Wellcome Trust Sanger Institute.  ...  Ab initio prediction does have its place in the Ensembl annotation system, as described below.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1858004">doi:10.1101/gr.1858004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15123590">pmid:15123590</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC479124/">pmcid:PMC479124</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mv4ydetsa5cchjycjibzlrynuu">fatcat:mv4ydetsa5cchjycjibzlrynuu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722180416/https://genome.cshlp.org/content/14/5/942.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/34/e1340e4403128f154d41864119b0e906c0bf46a9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1858004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC479124" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Ensembl genome database project

T. Hubbard
<span title="2002-01-01">2002</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.  ...  The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome.  ...  The Ensembl project is principally funded by the Wellcome Trust with additional funding from EMBL.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/30.1.38">doi:10.1093/nar/30.1.38</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11752248">pmid:11752248</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC99161/">pmcid:PMC99161</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u2fj5iq6tfga7kj7xrc3bk3su4">fatcat:u2fj5iq6tfga7kj7xrc3bk3su4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060116233426/http://monitor.admin.musc.edu:80/~cfs/molbio_tools/Ensembl_paper.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ee/0e/ee0e77cf1b0df5353318ac2433b5d9009785bcb6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/30.1.38"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ensembl 2004

E. Birney
<span title="2004-01-01">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements  ...  The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites.  ...  The Ensembl project is funded principally by the Wellcome Trust with additional funding from EMBL and NIH-NIAID.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkh038">doi:10.1093/nar/gkh038</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14681459">pmid:14681459</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC308772/">pmcid:PMC308772</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z3o4nydd4faopfzpufz5lfszi4">fatcat:z3o4nydd4faopfzpufz5lfszi4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050302063546/http://nar.oupjournals.org:80/cgi/reprint/32/suppl_1/D468.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/50/52/5052d33b44fee2ca6930972d91fa7d0ba0f80e6b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkh038"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308772" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements

Sung Doh, Yunyu Zhang, Matthew H Temple, Li Cai
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Here we describe the development of a web-based non-coding sequence retrieval system. Results: This paper presents a Non-Coding Sequences Retrieval System (NCSRS).  ...  The NCSRS is a web-based bioinformatics tool that performs fast and convenient retrieval of non-coding and coding sequences from multiple species related to a specific gene or set of genes.  ...  A table with links to NCBI, UCSC genome browser and Ensembl for the gene and specific species is also provided.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-94">doi:10.1186/1471-2105-8-94</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17362514">pmid:17362514</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1838437/">pmcid:PMC1838437</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p2qqum73b5eyjaxdji2htldsdi">fatcat:p2qqum73b5eyjaxdji2htldsdi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830115131/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-8-94?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/69/fa/69fa62cb8c15648df94709e93a6c7f9d8c88e988.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-94"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838437" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ensembl 2005

T. Hubbard
<span title="2004-12-17">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The majority have been annotated automatically using the Ensembl gene build system, showing its flexibility to reliably annotate a wide variety of genomes.  ...  The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences.  ...  ACKNOWLEDGEMENTS The Ensembl project is principally funded by the Wellcome Trust with additional funding from EMBL, NIH-NIAID and BBSRC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki138">doi:10.1093/nar/gki138</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15608235">pmid:15608235</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC540092/">pmcid:PMC540092</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7kdjynjp2jgl5j36hici5rteme">fatcat:7kdjynjp2jgl5j36hici5rteme</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726191959/https://watermark.silverchair.com/gki138.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaowggGmBgkqhkiG9w0BBwagggGXMIIBkwIBADCCAYwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMUUkqf1GOr3uw_tYRAgEQgIIBXQaUwR9x-0MTp5gBs6-X4NBkH8P_u0jfGtVNKQyfXgmcShSoaNHrfTLWDu9DtTCpDKjT0yDEmQa4ZnDRWQD4nsQ9l59NGjkr36_Jzf_lcQuArFElQjCFRdjr2kWzG_rTInj812jjFMS3tej85ZNaI40vbmOjDNbtGCN5sSHAedmjQubYHnVFWU6PnhNEYZ3YwDiDqnCmAYQV5sHpYuMy4AnOuYMPE0w_e_InO-HWdQtlwgCORD9oNNand9pK-SUJYH6XZ6pA-BVEhCg68jiVEncCdF5RTIiRw1KWl2UGHJ8dNiPFkeGdfdxCwztb6xqp36BwEEhQeY0FAOxOiBVOOgH3KXiE8Ypp1-zXhJgaqTHAM7Sa6XKsZQX-rh3TH9jF4VhOCJw3ywTOFWGXN-VC8bN_xZNgOv4OXptVDt10KAFTOh73rnW5YcQ9VkLxZtIqXczx0ar0zuXtBNuepSk" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e3/0f/e30fdfc5d1ca30d3b85a6e1519ce9008b5a8a32f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki138"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540092" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Otter Annotation System

S. M.J. Searle
<span title="2004-05-01">2004</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
We call the system that has been developed the Otter manual-annotation system.  ...  As annotators are not currently providing this, we have not supported it in the format. Figure 5 Ensembl gene predictions and otter annotations displayed in Apollo.  ...  We particularly acknowledge the members of the annotation team at the Wellcome Trust Sanger Institute and the Apollo development team at Berkeley and Harvard.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1864804">doi:10.1101/gr.1864804</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15123593">pmid:15123593</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC479127/">pmcid:PMC479127</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vyznwbjhvndwboedpenhy5q7xq">fatcat:vyznwbjhvndwboedpenhy5q7xq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722145848/https://genome.cshlp.org/content/14/5/963.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9a/14/9a14700d91117e647051cc1549039d4dd08b09d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1864804"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC479127" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An Overview of Ensembl

E. Birney
<span title="2004-05-01">2004</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
emerged from the key ideas and model systems of classical genetics.  ...  T his latest book by Elof Carlson is a first history of classical genetics, the era in which the chromosome theory of heredity was proposed and developed.  ...  Ensembl is no different, and when the term "annotation" is used subsequently, the focus is the definition of gene transcripts.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1860604">doi:10.1101/gr.1860604</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15078858">pmid:15078858</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC479121/">pmcid:PMC479121</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qdzew6me25fd5ikizpyzal2kb4">fatcat:qdzew6me25fd5ikizpyzal2kb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722171309/https://genome.cshlp.org/content/14/5/925.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0a/e8/0ae83545d40ce9f97839a3e4c5c9677e3f7104b8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1860604"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC479121" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PomBase: a comprehensive online resource for fission yeast

V. Wood, M. A. Harris, M. D. McDowall, K. Rutherford, B. W. Vaughan, D. M. Staines, M. Aslett, A. Lock, J. Bahler, P. J. Kersey, S. G. Oliver
<span title="2011-10-28">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access.  ...  PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community.  ...  ACKNOWLEDGEMENTS The authors thank members of the Ensembl and Ensembl Genomes teams for contributions to the PomBase data pipelines.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr853">doi:10.1093/nar/gkr853</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22039153">pmid:22039153</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245111/">pmcid:PMC3245111</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g346pl5zdrdq7bv7wwyhu2lgia">fatcat:g346pl5zdrdq7bv7wwyhu2lgia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225154328/http://pdfs.semanticscholar.org/7071/d81573c9d637e586f87b2fd5169575432430.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/71/7071d81573c9d637e586f87b2fd5169575432430.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr853"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245111" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome annotation techniques: new approaches and challenges

Alistair G. Rust, Emmanuel Mongin, Ewan Birney
<span title="">2002</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q2rzh4rosrd2rhrlmpfocas4qa" style="color: black;">Drug Discovery Today</a> </i> &nbsp;
Acknowledgements We would like to thank the the Ensembl team for many useful discussions and suggestions during the preparation of this review.  ...  Thanks also to Mark Robinson of the Biocomputation Group at the University of Hertfordshire, UK, for help in the formatting of Fig. 3 .  ...  The screenshot is taken from the Ensembl Contigview page, displaying predictions for the human gene RBL1 (Ensembl gene ID ENSG00000080839 in release 3.26.1).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-6446(02)02289-4">doi:10.1016/s1359-6446(02)02289-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12047883">pmid:12047883</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4vcrouyq6jbjvkrmpncja6jtbu">fatcat:4vcrouyq6jbjvkrmpncja6jtbu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20111215160223/http://www.amizone.net:80/AdminAmizone/WebForms/SessionPlans/SessionPlans/f1070Genome%20Annotation.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/76/2c/762c3f022b47e8ff9e52013c138788ed5d4993b4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-6446(02)02289-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

EnsMart: A Generic System for Fast and Flexible Access to Biological Data

A. Kasprzyk
<span title="2003-12-12">2003</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
The system consists of a query-optimized database and interactive, user-friendly interfaces.  ...  These can be applied to many research problems, ranging from SNP selection for candidate gene screening, through cross-species evolutionary comparisons, to microarray annotation.  ...  We gratefully acknowledge contributions and continuous support from the other members of the Ensembl team and the suggestions and feedback from EnsMart users.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1645104">doi:10.1101/gr.1645104</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14707178">pmid:14707178</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC314293/">pmcid:PMC314293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u5twj5oxfncwjn2mkpicfx4hga">fatcat:u5twj5oxfncwjn2mkpicfx4hga</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722175435/https://genome.cshlp.org/content/14/1/160.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4b/1c/4b1c185aa4b0f14610e85dd4a5ad35b8a3be68df.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1645104"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC314293" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ensembl 2006

E. Birney
<span title="2006-01-01">2006</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation of large genome sequences.  ...  The year has also seen extensive improvements to both data analysis and presentation, with the introduction of a redesigned website, the addition of RNA gene and regulatory annotation and substantial improvements  ...  ACKNOWLEDGEMENTS The Ensembl project is principally funded by the Wellcome Trust with additional funding from EMBL, NIH-NIAID and BBSRC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj133">doi:10.1093/nar/gkj133</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16381931">pmid:16381931</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1347495/">pmcid:PMC1347495</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l4valhjsl5gm5ginxd2alqxd5a">fatcat:l4valhjsl5gm5ginxd2alqxd5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224141643/http://pdfs.semanticscholar.org/5680/9ac6d1f5662d307ea08104d16ab5b246380b.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/56/80/56809ac6d1f5662d307ea08104d16ab5b246380b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkj133"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347495" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The desktop genome

Colin Semple
<span title="2000-12-22">2000</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
The Ensembl software automatically produces and archives annotation of the draft human genome sequence.  ...  Content The Ensembl software automatically produces and archives annotation of the draft human genome sequence.  ...  Worst feature The Ensembl system is a work in progress and makes no claims to be a source of flawless data; in certain cases Ensembl annotation can be perplexing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2000-2-1-reports2001">doi:10.1186/gb-2000-2-1-reports2001</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tpayrgxvfrbinmowjem245lp4q">fatcat:tpayrgxvfrbinmowjem245lp4q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170816052405/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2000-2-1-reports2001?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/be/d4/bed42d900f155038602bfd4e37d8fcfb7cd8425e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2000-2-1-reports2001"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

A unified gene catalog for the laboratory mouse reference genome

Y. Zhu, J. E. Richardson, P. Hale, R. M. Baldarelli, D. J. Reed, J. M. Recla, R. Sinclair, T. B. K. Reddy, C. J. Bult
<span title="2015-06-18">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2wcheulsyvd7bott7zn35dhoti" style="color: black;">Mammalian Genome</a> </i> &nbsp;
We report here a semi-automated process by which mouse genome feature predictions and curated annotations (i.e.  ...  Acknowledgments The development of the fjoin algorithm and its application to building and maintaining a unified catalog of mouse genes was supported by NIH HG00330-P1.  ...  The authors thank all of the curators at NCBI and HAVANA for their collaborative efforts to improve annotations for the reference mouse genome. The authors thank Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00335-015-9571-1">doi:10.1007/s00335-015-9571-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26084703">pmid:26084703</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4534496/">pmcid:PMC4534496</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rxxquwdntbcvvdyngyfxnel2le">fatcat:rxxquwdntbcvvdyngyfxnel2le</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171008040257/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/00e/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjEwMDcvczAwMzM1LTAxNS05NTcxLTEucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/da/c5/dac502694ed0eca43e27901612c3d74b734e7d79.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00335-015-9571-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4534496" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ensembl 2002: accommodating comparative genomics

M. Clamp
<span title="2003-01-01">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Ensembl also integrates manually annotated gene structures from external sources where available.  ...  As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements  ...  ACKNOWLEDGEMENTS The Ensembl project is principally funded by the Wellcome Trust with additional funding from EMBL.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg083">doi:10.1093/nar/gkg083</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12519943">pmid:12519943</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC165530/">pmcid:PMC165530</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/742bdqhqpfecjh5zef5ehdu5pi">fatcat:742bdqhqpfecjh5zef5ehdu5pi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811171046/http://www.icgeb.res.in/whotdr/cd1/PreCourseReading/NAR_DB2003/38.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/eb/b2eb396b4252a18bc09c16bc19915d5ac9aa991e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg083"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC165530" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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