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Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

William McLaren, Bethan Pritchard, Daniel Rios, Yuan Chen, Paul Flicek, Fiona Cunningham
<span title="2010-06-18">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
In Ensembl, a web-based tool (the SNP Effect Predictor) and API interface can now functionally annotate variants in all Ensembl and Ensembl Genomes supported species.  ...  Availability: The Ensembl SNP Effect Predictor can be accessed via the Ensembl website at http://www.ensembl.org/.  ...  RESULTS The SNP Effect Predictor tool can be used to quickly and accurately predict the effects of variants on Ensembl-annotated transcripts.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq330">doi:10.1093/bioinformatics/btq330</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20562413">pmid:20562413</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2916720/">pmcid:PMC2916720</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xpu3rnfuo5e4bjxm32wpglhrlq">fatcat:xpu3rnfuo5e4bjxm32wpglhrlq</a> </span>
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Scripting Analyses of Genomes in Ensembl Plants [chapter]

Bruno Contreras-Moreira, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato, Astrid Gall, Paul Flicek
<span title="">2022</span> <i title="Springer US"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes.  ...  While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk.  ...  We also acknowledge all of the members of the Ensembl team for developing and maintaining the front-end and back-end software and infrastructure that underpins Ensembl Plants. Funding  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-0716-2067-0_2">doi:10.1007/978-1-0716-2067-0_2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35037199">pmid:35037199</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lx6odri4lvfrzkutlccjpuzgg4">fatcat:lx6odri4lvfrzkutlccjpuzgg4</a> </span>
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The Ensembl Variant Effect Predictor

William McLaren, Laurent Gil, Sarah E. Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham
<span title="2016-06-06">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions.  ...  It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.  ...  published Ensembl SNP Effect Predictor [23] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13059-016-0974-4">doi:10.1186/s13059-016-0974-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27268795">pmid:27268795</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4893825/">pmcid:PMC4893825</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lziduun2xnhpteudwo3utn4nyi">fatcat:lziduun2xnhpteudwo3utn4nyi</a> </span>
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The Ensembl Variant Effect Predictor [article]

William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R. S. Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham
<span title="2016-03-04">2016</span> <i title="Cold Spring Harbor Laboratory"> biorxiv/medrxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The Ensembl Variant Effect Predictor (VEP) is a powerful toolset for the analysis, annotation and prioritization of genomic variants, including in non-coding regions.  ...  The VEP accurately predicts the effects of sequence variants on transcripts, protein products, regulatory regions and binding motifs by leveraging the high quality, broad scope, and integrated nature of  ...  published Ensembl SNP Effect Predictor [23] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/042374">doi:10.1101/042374</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iviou4gwszbnddriubpy6txk5u">fatcat:iviou4gwszbnddriubpy6txk5u</a> </span>
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Sequence variants from whole genome sequencing a large group of Icelanders

Daniel F Gudbjartsson, Patrick Sulem, Hannes Helgason, Arnaldur Gylfason, Sigurjon A Gudjonsson, Florian Zink, Asmundur Oddson, Gisli Magnusson, Bjarni V Halldorsson, Eirikur Hjartarson, Gunnar Th. Sigurdsson, Augustine Kong (+5 others)
<span title="2015-03-25">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a577b42d4nfhddl7kurxnuyzem" style="color: black;">Scientific Data</a> </i> &nbsp;
20% of rare (DAF o 0.5%) SNPs and indels in coding regions, the most heavily studied parts of the genome, have been observed in the public databases.  ...  Features of our variant data, such as the transition/transversion ratio and the length distribution of indels, are similar to published reports.  ...  Acknowledgements We thank all the participants in this study. This study was performed in collaboration with Illumina. Author Contributions Additional information  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/sdata.2015.11">doi:10.1038/sdata.2015.11</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25977816">pmid:25977816</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4413226/">pmcid:PMC4413226</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6i6y6sn4ofgzblmqhdfito7b5a">fatcat:6i6y6sn4ofgzblmqhdfito7b5a</a> </span>
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Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools

S. Castellana, T. Mazza
<span title="2013-03-15">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The greatest challenges currently facing investigators are data interpretation and the development of strategies to identify the few gene-coding variants that actually cause or confer susceptibility to  ...  First, we have presented an updated review of these tools and their primary functionalities, focusing on those that are naturally prone to analyze massive variant sets, to infer some interesting similarities  ...  'Variant Effect Predictor' (VEP) [14] is provided by Ensembl as a web-based service with Perl scripts and application programming interface (API).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbt013">doi:10.1093/bib/bbt013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23505257">pmid:23505257</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xwo4m7nj55auvb6ifozbvtg6l4">fatcat:xwo4m7nj55auvb6ifozbvtg6l4</a> </span>
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Gramene 2016: comparative plant genomics and pathway resources

Marcela K. Tello-Ruiz, Joshua Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule (+20 others)
<span title="2015-11-08">2015</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;
Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases).  ...  Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants.  ...  We would also like to thank the Cold Spring Harbor Laboratory (CSHL) and the Dolan DNA Learning Center, the Center for Genome Research and Biocomputing (CGRB) at Oregon State University, and the Ontario  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1179">doi:10.1093/nar/gkv1179</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26553803">pmid:26553803</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702844/">pmcid:PMC4702844</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q6fdmpjqxnarxerc6qokt6i6ui">fatcat:q6fdmpjqxnarxerc6qokt6i6ui</a> </span>
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NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels

Jens Aßmus, Armin O. Schmitt, Ralf H. Bortfeldt, Gudrun A. Brockmann
<span title="">2011</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q4ydiqfw2vbdhaiqvqusudjtmi" style="color: black;">Advances in Bioinformatics</a> </i> &nbsp;
In a second step, each variant is classified into one of 15 SNP classes or 19 InDel classes.  ...  NovelSNPer is based upon the gene structure information stored in Ensembl. It processes two million SNPs in six hours. The tool can be used online or downloaded.  ...  Acknowledgment The authors thank S. Hennig (ImaGenes GmbH, Berlin, Germany) for fruitful discussions and the Ensembl helpdesk team for valuable advice.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2011/657341">doi:10.1155/2011/657341</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22110502">pmid:22110502</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3206323/">pmcid:PMC3206323</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z3jeijw46nhn3g6tk3l54smfjm">fatcat:z3jeijw46nhn3g6tk3l54smfjm</a> </span>
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Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

S. Mooney
<span title="2005-01-01">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Since the initial sequencing of the human genome, many projects are underway to understand the effects of genetic variation between individuals.  ...  Bioinformaticians have become very good at functional inference methods derived from functional and structural genomics.  ...  efforts to predict variation that is likely to have a functional effect (and possibly a phenotypic effect) and to classify the downstream molecular effects of those variants.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/6.1.44">doi:10.1093/bib/6.1.44</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15826356">pmid:15826356</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/okbeyyns6nda7ogkiqxiynuk24">fatcat:okbeyyns6nda7ogkiqxiynuk24</a> </span>
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Computational approaches to interpreting genomic sequence variation

Graham RS Ritchie, Paul Flicek
<span title="2014-10-22">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odidfbcgarekjpyyfxpdptajxa" style="color: black;">Genome Medicine</a> </i> &nbsp;
Here, we review and assess the limitations of computational techniques for categorizing variants according to functional classes, prioritizing variants for experimental follow-up and generating hypotheses  ...  3 million or so variants expected in an individual genome.  ...  Acknowledgements We thank Spencer Phillips for assistance with the figures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-014-0087-1">doi:10.1186/s13073-014-0087-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25473426">pmid:25473426</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4254438/">pmcid:PMC4254438</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xu4wzn37wzcljiuh2vaa2asm2m">fatcat:xu4wzn37wzcljiuh2vaa2asm2m</a> </span>
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PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants

Tochukwu C. Ofoegbu, Alessia David, Lawrence A. Kelley, Stefans Mezulis, Suhail A. Islam, Sophia F. Mersmann, Léonie Strömich, Ilya A. Vakser, Richard S. Houlston, Michael J.E. Sternberg
<span title="2019-05-07">2019</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
as input, genomic coordinates formats (Ensembl, VCF, reference SNP ID and HGVS notations) and Human Build GRCh37 and GRCh38.  ...  PhyreRisk is an open-access, publicly accessible web application for interactively bridging genomic, proteomic and structural data facilitating the mapping of human variants onto protein structures.  ...  Service interface to programmatically query the Ensembl Variant Effect Predictor (VEP) [21] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2019.04.043">doi:10.1016/j.jmb.2019.04.043</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31075275">pmid:31075275</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6597944/">pmcid:PMC6597944</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pce6d4goprgrdbxj6iswkklugi">fatcat:pce6d4goprgrdbxj6iswkklugi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428135625/https://kuscholarworks.ku.edu/bitstream/handle/1808/30877/Ofoegbu_2019.pdf;jsessionid=EBA02C2052C740A02EB46D146DBA783A?sequence=1" 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/6a/73/6a7304c8dd8e4ae540a34da989647c9be3aa9c8b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jmb.2019.04.043"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6597944" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Supplementary materials from Stochastic processes drive rapid genomic divergence during experimental range expansions

Christopher Weiss-Lehman, Silas Tittes, Nolan C. Kane, Ruth A. Hufbauer, Brett A. Melbourne
<span title="2019-03-20">2019</span> <i title="Figshare"> Figshare </i> &nbsp;
All supplementary methods, results, and figures  ...  McLaren W et al. 2010 Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069-2070. 49.  ...  McLaren W et al. 2016 The ensembl variant effect predictor. Genome biology 17, 122. 50. Stern C. 1943 The Hardy-Weinberg law. Science 97, 137-138.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.7867850.v1">doi:10.6084/m9.figshare.7867850.v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3onvm7m4xjfuvmgitevjuyzkpq">fatcat:3onvm7m4xjfuvmgitevjuyzkpq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211094931/https://s3-eu-west-1.amazonaws.com/pstorage-rs-4828782598/14651687/rspb20190231_si_001.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/fe/17/fe172a97dd8c2f97f26b75bebde3eda5fffbf2af.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.7867850.v1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

Predicting the functional consequences of non-synonymous DNA sequence variants — evaluation of bioinformatics tools and development of a consensus strategy

Kimon Frousios, Costas S. Iliopoulos, Thomas Schlitt, Michael A. Simpson
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/z3egmghp4rdu7dxxr3ldohtkma" style="color: black;">Genomics</a> </i> &nbsp;
In this study we evaluate the performance of nine such methods (SIFT, PolyPhen2, SNPs&GO, PhD-SNP, PANTHER, Mutation Assessor, MutPred, Condel and CAROL) and developed CoVEC (Consensus Variant Effect Classification  ...  Even within protein coding regions of the genome, establishing the consequences of variation on gene and protein function is challenging and requires substantial laboratory investigation.  ...  The task of obtaining functional effect predictions from multiple tools can be simplified with the use of meta-tools such as PON-P [24] and the Ensembl SNP Effect Predictor [22] , both of which serve  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ygeno.2013.06.005">doi:10.1016/j.ygeno.2013.06.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23831115">pmid:23831115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/23jjrtreebhi5igv24od33hplu">fatcat:23jjrtreebhi5igv24od33hplu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190322183056/https://core.ac.uk/download/pdf/82546634.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/6f/80/6f80923199b3e5692847e96c7850a0976defcc7a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ygeno.2013.06.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Ensembl 2020

<span title="2020-01-08">2019</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;
Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227.  ...  The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key  ...  ACKNOWLEDGEMENTS We wish to thank all of our user community and data providers for making their data available for reuse within Ensembl.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz966">doi:10.1093/nar/gkz966</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31691826">pmid:31691826</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7145704/">pmcid:PMC7145704</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i5tdgfqtd5dn7by55qjej2dade">fatcat:i5tdgfqtd5dn7by55qjej2dade</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200503200652/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7145704&amp;blobtype=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/bf/58/bf58e5a2e188c474f725f21eb1701a7ae619dab2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz966"> <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/PMC7145704" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Gramene database: Navigating plant comparative genomics resources

Parul Gupta, Sushma Naithani, Marcela Karey Tello-Ruiz, Kapeel Chougule, Peter D'Eustachio, Antonio Fabregat, Yinping Jiao, Maria Keays, Young Koung Lee, Sunita Kumari, Joseph Mulvaney, Andrew Olson (+10 others)
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m3p3hvzakffdxnyoguxabfvqbm" style="color: black;">Current Plant Biology</a> </i> &nbsp;
Here we briefly describe the functions and uses of the Gramene database.  ...  It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species.  ...  of the resources and tools.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpb.2016.12.005">doi:10.1016/j.cpb.2016.12.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28713666">pmid:28713666</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5509230/">pmcid:PMC5509230</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gmdx6rggmjgpbptvme75fmf7d4">fatcat:gmdx6rggmjgpbptvme75fmf7d4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209085108/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5509230&amp;blobtype=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/46/dc/46dcc3cab6ce6cc4afc59848040f4cda134e9cb5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cpb.2016.12.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5509230" 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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