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The UCSC Genome Browser Database: update 2006
2006
Nucleic Acids Research
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The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. ...
The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. ...
ACKNOWLEDGEMENTS The UCSC GBD project is funded by grants from the National Human Genome Research Institute (NHGRI), the Howard Hughes Medical Institute (HHMI) and the National Cancer Institute (NCI). ...
doi:10.1093/nar/gkj144
pmid:16381938
pmcid:PMC1347506
fatcat:fdhl3rwlpnclnox2lrd3k7e7se
The UCSC Genome Browser database: 2016 update
2015
Nucleic Acids Research
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The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. ...
Genome Browser wiki site. ...
We would also like to acknowledge the dedicated system administrators who have provided an excellent ...
doi:10.1093/nar/gkv1275
pmid:26590259
pmcid:PMC4702902
fatcat:vpehyk3xujegfhqlaq7znr5rgi
The UCSC Archaeal Genome Browser
2006
Nucleic Acids Research
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The feature-rich UCSC Genome Browser, created originally to annotate the human genome, can be applied to any sequenced organism. ...
We have created a UCSC Archaeal Genome Browser, available at http://archaea.ucsc.edu/, currently with 26 archaeal genomes. ...
ACKNOWLEDGEMENTS We thank Jim Kent and the Genome Bioinformatics Group of UC Santa Cruz, in particular Hiram Clawson, for providing the UCSC Genome Browser and assisting us in developing the Archaeal Genome ...
doi:10.1093/nar/gkj134
pmid:16381898
pmcid:PMC1347496
fatcat:p3p5d4jb5jfenhbokwzygyo7jm
The UCSC Archaeal Genome Browser: 2012 update
2011
Nucleic Acids Research
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The genome browser environment maintains the current look-and-feel of the vertebrate UCSC Genome Browser, but also integrates archaeal and bacterial-specific tracks with a few graphic display enhancements ...
The UCSC Archaeal Genome Browser (http:// archaea.ucsc.edu) offers a graphical web-based resource for exploration and discovery within archaeal and other selected microbial genomes. ...
ACKNOWLEDGEMENTS We thank Jim Kent and the Genome Bioinformatics Group of UC Santa Cruz for providing us with excellent assistance in developing the Archaeal Genome Browser. ...
doi:10.1093/nar/gkr990
pmid:22080555
pmcid:PMC3245099
fatcat:nbatgfqcjbfqbbwg7a5alvbcyq
The UCSC SARS-CoV-2 Genome Browser
[article]
2020
bioRxiv
pre-print
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Results: The UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID ...
We adapted our genome browser visualization tool to the viral genome for this purpose. ...
Armenta, Phil Berman, Nik Sgourakis and the rest of the scientists at UCSC and across the world for making these tracks of molecular information possible. ...
doi:10.1101/2020.05.04.075945
fatcat:yqmldbtnwbe43mb4yftpzy4ubi
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
2007
Genome Research
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Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability ...
and analyzed with the Galaxy server at http://g2.bx.psu.edu. This paper illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. ...
Sudhir Kumar and the reviewers provided many useful suggestions. Additional help was provided by Cathy Riemer and Heather Lawson. ...
doi:10.1101/gr.6761107
pmid:17984227
pmcid:PMC2099589
fatcat:dbrzsps2hzcztchnbfe6ro7yia
Automated Querying of Genome Databases
2007
PLoS Computational Biology
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The authors received no specific funding for this article. Competing interests. The author has declared that no competing interests exist. ...
UCSC Genome Browser Databases. ...
table with the appropriate UCSC SNP table (e.g., table ''snp126'' for the March 2006 build of the UCSC database). ...
doi:10.1371/journal.pcbi.0030001
pmid:17257048
pmcid:PMC1782033
fatcat:myarq5e5szhkjfuuswt3jye6z4
Choosing a genome browser for a Model Organism Database: surveying the Maize community
2010
Database: The Journal of Biological Databases and Curation
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we could not have created an implementation of the MaizeGDB Genome Browser customized to support our users' needs. ...
We thank the anonymous reviewers whose suggestions helped us improve this article. We very much appreciate the useful comments by Dr Patrick Armstrong. ...
The UCSC genome browser database The University of California Santa Cruz (UCSC) Genome Browser Database (28) started as part of the Human Genome Project (41) to make newly generated human genomic sequences ...
doi:10.1093/database/baq007
pmid:20627860
pmcid:PMC2911842
fatcat:6ihbvxcmdnfypo2clanjfma5vq
MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains
2009
Nucleic Acids Research
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The results of such queries are presented either as a custom track on the UCSC mouse genome browser or in tabular format. ...
We anticipate that the MouseIndelDB database will be widely useful for research in mammalian genetics, genomics, and evolutionary biology. Access to the MouseIndelDB database is ...
Custom track at UCSC mouse genome browser We implemented a custom track at the UCSC mouse genome browser (43) to display content of the MouseIndelDB database in the context of other annotated genomic ...
doi:10.1093/nar/gkp1046
pmid:19933259
pmcid:PMC2808983
fatcat:3zc5kjfrmjfh3isphkpc24s3sy
dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans
2006
Human Mutation
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In dbRIP, we deploy the utilities and annotated data of the genome browser developed at the University of California at Santa Cruz (UCSC) for user-friendly queries and integrative browsing of RIPs along ...
Communicated by Alastair Brown Retrotransposons constitute over 40% of the human genome and play important roles in the evolution of the genome. ...
We thank all researchers who have contributed to the RIP data, especially those who posted their full datasets online. ...
doi:10.1002/humu.20307
pmid:16511833
pmcid:PMC1855216
fatcat:jmfx4pxh2vanpf4rnxl2ydx5gy
circBase: a database for circular RNAs
2014
RNA: A publication of the RNA Society
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We developed a database and website, "circBase," where merged and unified data sets of circRNAs and the evidence supporting their expression can be accessed, downloaded, and browsed within the genomic ...
The database is freely accessible through the web server at http://www.circbase.org/. ...
P.G. was partially funded by the DFG Graduate School "Computational Systems Biology" (CSB-GRK 1772) and DEEP-German Epigenome Programme. P.P. was funded by the MDC-NYU PhD Exchange Programme. ...
doi:10.1261/rna.043687.113
pmid:25234927
pmcid:PMC4201819
fatcat:lncyv4yhivapvd6qbja6plwqgm
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
2007
Nucleic Acids Research
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We have greatly expanded the Alternative Splicing Annotation Project (ASAP) database: (i) its human alternative splicing data are expanded 3-fold over the previous ASAP database, to nearly 90 000 distinct ...
for comparing alternative splicing and splice site conservation across 17 aligned genomes, based on UCSC multigenome alignments; (iv) it provides an 2-to 3-fold expansion in detection of tissue-specific ...
ACKNOWLEDGEMENTS The authors wish to thank Calvin Pan, Qi Wang and Dr Yi Xing for valuable comments on this work. ...
doi:10.1093/nar/gkl884
pmid:17108355
pmcid:PMC1669709
fatcat:va56pn3oajakrdwisrpgqbdnbi
Updates of the HbVar database of human hemoglobin variants and thalassemia mutations
2013
Nucleic Acids Research
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to the continuous improvement of the database profile and contents. ...
ACKNOWLEDGEMENTS The authors thank all the HbVar users worldwide for their valuable comments and suggestions, which help us to keep the information as updated and complete as possible and also contribute ...
at Santa Cruz (UCSC) Genome Browser (10) and the Pennsylvania State University Genome Browsers, using the dedicated HbVar custom tracks ( Figure 2 ). ...
doi:10.1093/nar/gkt911
pmid:24137000
pmcid:PMC3964999
fatcat:v5lxlyw7a5dstadjq2iewriz6e
miRvar: A comprehensive database for genomic variations in microRNAs
2011
Human Mutation
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The data is made available on the Leiden Open (source) Variation Database (LOVD) platform at http://genome.igib.res.in/mirlovd to provide ease of aggregation and analysis and is open for community curation ...
We have comprehensively curated genetic variations in miRNA loci in the human genome and established a computational pipeline to assess potential functional consequences of these variants along with methods ...
Saakshi Jalali for evaluating the database and Mr. Hemant Suryawanshi for his valuable inputs. ...
doi:10.1002/humu.21482
pmid:21618345
fatcat:tnfht5hac5hupmuiar7lh473t4
A searchable database of genetic evidence for psychiatric disorders
2008
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics
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Findings can be save to disk or viewed via a genome browser. ...
SLEP is a searchable archive of findings from psychiatric genetics that is freely available on the web for non-commercial use (http://slep.unc.edu). ...
Acknowledgments HF was supported by K07 CA118412 (Anna Helena Furberg Barnes) from the National Cancer Institute. ...
doi:10.1002/ajmg.b.30802
pmid:18548508
pmcid:PMC2574546
fatcat:ebcx7dhifje6riqqrrrqbn5phm
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