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The UCSC Genome Browser Database: update 2006

A. S. Hinrichs
2006 Nucleic Acids Research  
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

Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steve Heitner, Rachel A. Harte (+11 others)
2015 Nucleic Acids Research  
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

K. L. Schneider
2006 Nucleic Acids Research  
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

P. P. Chan, A. D. Holmes, A. M. Smith, D. Tran, T. M. Lowe
2011 Nucleic Acids Research  
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]

Jason D Fernandes, Angie S Hinrichs, Hiram Clawson, Jairo Navarro Gonzales, Brian T Lee, Luis R Nassar, Brian J Raney, Kate R Rosenbloom, Santrupti Nerli, Arjun A Rao, Daniel Schmelter, Ann S Zweig (+6 others)
2020 bioRxiv   pre-print
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

W. Miller, K. Rosenbloom, R. C. Hardison, M. Hou, J. Taylor, B. Raney, R. Burhans, D. C. King, R. Baertsch, D. Blankenberg, S. L. Kosakovsky Pond, A. Nekrutenko (+14 others)
2007 Genome Research  
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

Peter Schattner
2007 PLoS Computational Biology  
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

Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence
2010 Database: The Journal of Biological Databases and Curation  
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

K. Akagi, R. M. Stephens, J. Li, E. Evdokimov, M. R. Kuehn, N. Volfovsky, D. E. Symer
2009 Nucleic Acids Research  
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

Jianxin Wang, Lei Song, Deepak Grover, Sami Azrak, Mark A. Batzer, Ping Liang
2006 Human Mutation  
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

Petar Glažar, Panagiotis Papavasileiou, Nikolaus Rajewsky
2014 RNA: A publication of the RNA Society  
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

N. Kim, A. V. Alekseyenko, M. Roy, C. Lee
2007 Nucleic Acids Research  
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

Belinda Giardine, Joseph Borg, Emmanouil Viennas, Cristiana Pavlidis, Kamran Moradkhani, Philippe Joly, Marina Bartsakoulia, Cathy Riemer, Webb Miller, Giannis Tzimas, Henri Wajcman, Ross C. Hardison (+1 others)
2013 Nucleic Acids Research  
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

Deeksha Bhartiya, Saurabh V. Laddha, Arijit Mukhopadhyay, Vinod Scaria
2011 Human Mutation  
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

Thomas Konneker, Todd Barnes, Helena Furberg, Molly Losh, Cynthia M. Bulik, Patrick F. Sullivan
2008 American Journal of Medical Genetics Part B: Neuropsychiatric Genetics  
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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