The UCSC Genome Browser database: 2016 update

For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the “Data Integrator”, for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype- and disease-associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.

[1]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[2]  Alejandro A. Schäffer,et al.  WindowMasker: window-based masker for sequenced genomes , 2006, Bioinform..

[3]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[4]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Jun S. Liu,et al.  The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans , 2015, Science.

[6]  Melissa J. Landrum,et al.  RefSeq: an update on mammalian reference sequences , 2013, Nucleic Acids Res..

[7]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[8]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[9]  Eric W Deutsch,et al.  The state of the human proteome in 2012 as viewed through PeptideAtlas. , 2013, Journal of proteome research.

[10]  Tim J. P. Hubbard,et al.  Dalliance: interactive genome viewing on the web , 2011, Bioinform..

[11]  Philip Lijnzaad,et al.  The Ensembl genome database project , 2002, Nucleic Acids Res..

[12]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[13]  P. Stenson,et al.  The Human Gene Mutation Database: 2008 update , 2009, Genome Medicine.

[14]  Jeroen F. J. Laros,et al.  LOVD v.2.0: the next generation in gene variant databases , 2011, Human mutation.

[15]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[16]  L. Stein,et al.  Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome , 2012, Cancers.

[17]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[18]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[19]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[20]  Mario Stanke,et al.  Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.

[21]  S. Karlin,et al.  Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.

[22]  D. Haussler,et al.  Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[23]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[24]  Brian T. Lee,et al.  The UCSC Genome Browser database: 2015 update , 2014, Nucleic Acids Res..

[25]  Jeffrey R. Whiteaker,et al.  Proteogenomic characterization of human colon and rectal cancer , 2014, Nature.

[26]  María Martín,et al.  UniProt: A hub for protein information , 2015 .

[27]  Eric W. Deutsch,et al.  The PeptideAtlas project , 2005, Nucleic Acids Res..

[28]  Jon W. Huss,et al.  BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources , 2009, Genome Biology.

[29]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[30]  G. Bejerano,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[31]  Jim Thurmond,et al.  FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations , 2014, Nucleic Acids Res..

[32]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[33]  Marc Via i García.  An integrated map of genetic variation from 1,092 human genomes , 2012 .

[34]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[35]  Patricia P. Chan,et al.  GtRNAdb: a database of transfer RNA genes detected in genomic sequence , 2008, Nucleic Acids Res..

[36]  David Haussler,et al.  Using native and syntenically mapped cDNA alignments to improve de novo gene finding , 2008, Bioinform..

[37]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[38]  David Haussler,et al.  The UCSC Known Genes , 2006, Bioinform..

[39]  David Haussler,et al.  ENCODE Data in the UCSC Genome Browser: year 5 update , 2012, Nucleic Acids Res..

[40]  Jonathan M. Mudge,et al.  The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. , 2009, Genome research.

[41]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[42]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[43]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[44]  Huaiyu Mi,et al.  The InterPro protein families database: the classification resource after 15 years , 2014, Nucleic Acids Res..

[45]  Galt P. Barber,et al.  BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..

[46]  Heidi L Rehm,et al.  ClinGen--the Clinical Genome Resource. , 2015, The New England journal of medicine.

[47]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[48]  Ting Wang,et al.  Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser , 2013, Bioinform..

[49]  David Haussler,et al.  Navigating protected genomics data with UCSC Genome Browser in a Box , 2014, Bioinform..

[50]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[51]  Daniel Rios,et al.  Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .

[52]  David Haussler,et al.  The Human Epigenome Browser at Washington University , 2011, Nature Methods.

[53]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[54]  Robert D. Finn,et al.  Rfam 12.0: updates to the RNA families database , 2014, Nucleic Acids Res..

[55]  D. Haussler,et al.  Exploring relationships and mining data with the UCSC Gene Sorter. , 2005, Genome research.

[56]  D. Haussler,et al.  Aligning multiple genomic sequences with the threaded blockset aligner. , 2004, Genome research.

[57]  Joaquín Dopazo,et al.  PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes , 2005, Nucleic Acids Res..

[58]  K. Pollard,et al.  Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.

[59]  L. B. Snoek,et al.  Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856 , 2015, Genetics.

[60]  A. Nekrutenko,et al.  Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences , 2010, Genome Biology.