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GENCODE reference annotation for the human and mouse genomes
2018
Nucleic Acids Research
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The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics ...
Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. ...
ACKNOWLEDGEMENTS We thank Tim Hubbard and Jennifer Harrow for their leadership in the GENCODE project from 2003-2016 as well as all groups and group members involved in the GENCODE project since its inception ...
doi:10.1093/nar/gky955
pmid:30357393
pmcid:PMC6323946
fatcat:vg5kuecy5rc7xewce5u3xczdba
GENCODE 2021
2020
Nucleic Acids Research
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reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. ...
The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics ...
of the human and mouse reference genomes. ...
doi:10.1093/nar/gkaa1087
pmid:33270111
pmcid:PMC7778937
fatcat:eqyplhdexbdchn53omyqjckpge
Creating reference gene annotation for the mouse C57BL6/J genome assembly
2015
Mammalian Genome
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Annotation on the reference genome of the C57BL6/J mouse has been an ongoing project ever since the draft genome was first published. ...
Here, we describe the progress of the GENCODE mouse annotation project, which combines manual annotation from the HAVANA group with Ensembl computational annotation, alongside experimental and in silico ...
, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. ...
doi:10.1007/s00335-015-9583-x
pmid:26187010
pmcid:PMC4602055
fatcat:y5eenrzsdnfr5jdy6wezb6etm4
Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation
[article]
2017
bioRxiv
pre-print
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We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. ...
The result is an explosion of new, ultra-contiguous genome assemblies. To compare these genomes we need robust methods for genome annotation. ...
Finally, we would like to thank Fergal Martin and Paul Flicek for revising the paper and providing a pre-release of the Ensembl V91 annotations on chimpanzee and gorilla, as well as the whole GENCODE consortium ...
doi:10.1101/231118
fatcat:y4acyavz2rgf5ceaxqx7cowoze
Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA
2006
Genome Biology
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This is illustrated in the EGASP project, where reference annotations against which all automatic methods are measured are generated by human annotators and experimentally verified. ...
We discuss current limitations of the method and several avenues for improvement. ...
Acknowledgments We wish to thank Paul Flicek for kindly providing an updated version of the Eval software, Matthieu Muffato for assistance with engineering aspects and Fiona Francis for critical reading ...
doi:10.1186/gb-2006-7-s1-s7
pmid:16925841
pmcid:PMC1810556
fatcat:hmzww44ejfezvgcvamarblbib4
APPRIS 2017: principal isoforms for multiple gene sets
2017
Nucleic Acids Research
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In addition AP-PRIS now provides a measure of reliability for individual principal isoforms and updates with each release of the GENCODE/Ensembl and RefSeq reference sets. ...
The individual GENCODE/Ensembl, Ref-Seq and UniProtKB reference gene sets for six organisms have been merged to produce common sets of splice variants. ...
For that reason we have extended APPRIS to the RefSeqGene and UniProtKB annotations in the case of vertebrate genomes (human, mouse, zebra-fish, rat, pig and chimpanzee). ...
doi:10.1093/nar/gkx997
pmid:29069475
pmcid:PMC5753224
fatcat:dmhn5ropvnbtzoftrf4aoovvoe
Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
2018
Genome Research
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We show that CAT can be used to improve annotations on the rat genome, annotate the great apes, annotate a diverse set of mammals, and annotate personal, diploid human genomes. ...
The result is an explosion of new, ultracontiguous genome assemblies. To compare these genomes, we need robust methods for genome annotation. ...
Finally, we thank Fergal Martin and Paul Flicek for revising the paper and providing a pre-release of the Ensembl V91 annotations on chimpanzee and gorilla, as well as the whole GENCODE Consortium for ...
doi:10.1101/gr.233460.117
pmid:29884752
fatcat:gtgabvlntfgxfg3h3wibuy3t2a
Ensembl 2017
2016
Nucleic Acids Research
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Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. ...
Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. ...
ACKNOWLEDGEMENTS Thank you to the Systems Administration teams at the Wellcome Trust Sanger Institute and at EMBL-EBI for ...
doi:10.1093/nar/gkw1104
pmid:27899575
pmcid:PMC5210575
fatcat:hzc4nlutrnfo5obbhqtlljr724
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts
2006
Genome Biology
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MARS uses the mouse, rat, dog, opossum, chicken, and frog genome sequences as pairwise informant sources for Twinscan and combines the resulting transcript predictions into genes based on coding (CDS) ...
alternatively spliced transcripts in the GENCODE annotation is relatively small. ...
MRB and the development of the Twinscan code base were supported in part by HG02278 from the National Human Genome Research Institute. ...
doi:10.1186/gb-2006-7-s1-s8
pmid:16925842
pmcid:PMC1810557
fatcat:4gjt2gdnofbvrbzjhusulitm64
The UCSC Genome Browser database: update 2011
2010
Nucleic Acids Research
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Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation ...
As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data ...
The GENCODE project provides high-quality manual curation of evidence-based automated gene predictions for human and mouse genomes. ...
doi:10.1093/nar/gkq963
pmid:20959295
pmcid:PMC3242726
fatcat:fnemefhmkbc65bmwbfxqlp7lpm
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
2019
Genome Research
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Here, we present the first whole-genome PhyloCSF prediction tracks for human, mouse, chicken, fly, worm, and mosquito. ...
The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. ...
Acknowledgments We thank Jade Vinson for help with splice prediction software, Lel Eory for help with chicken data, and Mike Lin, Clara Chan, Mark Diekhans, John Rinn, and Jennifer Harrow for helpful input ...
doi:10.1101/gr.246462.118
pmid:31537640
pmcid:PMC6886504
fatcat:3suhcry5dzfovlerm5f4egv7li
GENCODE: The reference human genome annotation for The ENCODE Project
2012
Genome Research
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The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. ...
GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. ...
Acknowledgments We thank all of the HAVANA team that contributed to the manual annotation and the Ensembl gene builders, and the VEGA team that produced the release of GENCODE. ...
doi:10.1101/gr.135350.111
pmid:22955987
pmcid:PMC3431492
fatcat:qnre6dj4fvbbxluelrhsww4mma
Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor
2007
Genomics
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The exon-intron structure of eukaryotic genes allows for phenomena such as alternative splicing, nonsense-mediated decay, and regulation through untranslated regions. ...
In this study, we use the phylogenetically diverse sequencing of the ENCODE regions to study gene structure evolution in mammalian genomes. ...
We also thank the GENCODE and HAVANA teams for organizing the EGASP workshop during which we began work on this project. ...
doi:10.1016/j.ygeno.2007.03.008
pmid:17499477
pmcid:PMC2034525
fatcat:ixdlfjlf2bcelczusj7bq6bspm
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
2014
Human Molecular Genetics
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Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. ...
We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort. ...
ACKNOWLEDGEMENTS The authors thank Daniel Rico for suggestions and discussions regarding gene expression and gene family age data. Conflict of Interest statement. None declared. ...
doi:10.1093/hmg/ddu309
pmid:24939910
pmcid:PMC4204768
fatcat:mnpjk63imrcffjiciswbdxntzq
High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing
[article]
2017
bioRxiv
pre-print
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We present an experimental re-annotation of the GENCODE intergenic lncRNA population in matched human and mouse tissues, resulting in novel transcript models for 3574 / 561 gene loci, respectively. ...
Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. ...
Genome-aligned data were assembled into a public Track Hub, which can be loaded into the UCSC Genome Browser (see URLs). ...
doi:10.1101/105064
fatcat:ufwxwaedc5dbhhbhrmneiawl3y
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