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The UCSC Genome Browser Database: update 2009
2009
Nucleic Acids Research
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The UCSC Genome Browser Database (GBD, http:// ...
We would also like to acknowledge the dedicated system administrators who have provided an excellent computing environment: Jorge Garcia, Erich Weiler, Chester Manuel and Victoria Lin. ...
ACKNOWLEDGEMENTS We would like to thank the many collaborators who have contributed data to our project, our Scientific Advisory Board for their valuable advice and recommendations, and our users for their ...
doi:10.1093/nar/gkn875
pmid:18996895
pmcid:PMC2686463
fatcat:gkmg6oyuc5fmjo46h422lvvqf4
The UCSC Genome Browser database: update 2010
2009
Nucleic Acids Research
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The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc .edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool ...
New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. ...
ACKNOWLEDGEMENTS We wish to thank the numerous collaborators worldwide who have contributed annotation data to the Genome Browser, the individuals on our Scientific Advisory Board who guide our work, and ...
doi:10.1093/nar/gkp939
pmid:19906737
pmcid:PMC2808870
fatcat:k3rf3riiznfexe3h7ydbhitysi
The UCSC Genome Browser database: update 2011
2010
Nucleic Acids Research
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Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome ...
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 ...
Other tools The UCSC Genome Browser website provides additional tools to access the database and complement the Genome Browser. ...
doi:10.1093/nar/gkq963
pmid:20959295
pmcid:PMC3242726
fatcat:fnemefhmkbc65bmwbfxqlp7lpm
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
2011
Nucleic Acids Research
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The Encyclopedia of DNA Elements (ENCODE) project is an international consortium of investigators funded to analyze the human genome with the goal of producing a comprehensive catalog of functional elements ...
The ENCODE Data ...
We also acknowledge Hiram Clawson, a core Genome Browser engineer who has contributed greatly to its overall success by his work to keep the browser reliable, fast and annotationrich. ...
doi:10.1093/nar/gkr1012
pmid:22075998
pmcid:PMC3245183
fatcat:nzoqo62bbrhyzccqsag5ngl7ey
The Mouse Genome Database: enhancements and updates
2009
Nucleic Acids Research
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The Mouse Genome Database (MGD) is a major component of the Mouse Genome Informatics (MGI, http://www.informatics.jax.org/) database resource and serves as the primary community model organism database ...
and genome variant information including comparative data on mammalian genes. ...
The staff of MGD collaborates with members of other large genome informatics resources including NCBI (http://www.informatics.jax.org), Ensembl (http://www .ensembl.org), UCSC Genome Browser (http://genome ...
doi:10.1093/nar/gkp880
pmid:19864252
pmcid:PMC2808942
fatcat:4azrklowubgqxfc7fogb5644ei
H-DBAS: human-transcriptome database for alternative splicing: update 2010
2009
Nucleic Acids Research
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In this update, for better annotations of AS events, we correlated RNA-Seq tag information to the AS exons and splice junctions. ...
We also present a new comparative genomics viewer so that users can empirically understand the evolutionary turnover of AS. ...
Sekimori for the technical support for RNA-Seq analysis, M. Nitta for constructing the comparative genomics viewer, and T. Endo for the technical support for server usage. ...
doi:10.1093/nar/gkp984
pmid:19969536
pmcid:PMC2808982
fatcat:gm4nmnbszbgmvpixzcjyc3nlri
The database of experimentally supported targets: a functional update of TarBase
2009
Nucleic Acids Research
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Additionally, the database is functionally linked to several other relevant and useful databases such as Ensembl, Hugo, UCSC and SwissProt. The TarBase5.0 database can be queried or downloaded from ...
Each target site is described by the miRNA that binds it, the gene in which it occurs, the nature of the experiments that were conducted to test it, the sufficiency of the site to induce translational ...
and the UCSC browser respectively. ...
doi:10.1093/nar/gkn809
pmid:18957447
pmcid:PMC2686456
fatcat:h7pbllklwje6pgcxpdoukx7avu
Rfam: updates to the RNA families database
2009
Nucleic Acids Research
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The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs. ...
A minority of families with a very broad taxonomic range (e.g. tRNA and rRNA) provide the majority of the sequence annotations, whilst the majority of Rfam families (e.g. snoRNAs and miRNAs) have a limited ...
ACKNOWLEDGEMENTS We would like to thank Ivo Hofacker and Andreas Gruber for secondary structure graphics code, and Zasha Weinberg, Jeffrey Barrick, Chris Brown, Tom Jones for contributions to the database ...
doi:10.1093/nar/gkn766
pmid:18953034
pmcid:PMC2686503
fatcat:b2nst2s35zcrxdcepwtmmmqmmy
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
2009
Nucleic Acids Research
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The latter is a UCSC Genome Browser mirror with large additional custom tracks specifically associated with noncoding elements. ...
The database combo is called the Functional RNA Database and consists of two databases: a rewrite of the original version of the Functional RNA Database (fRNAdb) and the latest version of the UCSC Geno-meBrowser ...
ACKNOWLEDGEMENTS The authors thank everyone in the bioinformatics group of the Functional RNA Project for constructive criticisms and fruitful discussions. ...
doi:10.1093/nar/gkn805
pmid:18948287
pmcid:PMC2686472
fatcat:5ap3uo42qnflbheznx65vhj2ge
ChimerDB 2.0—a knowledgebase for fusion genes updated
2009
Nucleic Acids Research
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The human genome map used for transcriptome analysis was the NCBI build 36.1 (hg18 in the UCSC genome browser database) (25) . Literature-related information was obtained as follows. ...
Links to the UCSC genome browser are provided to allow users to examine the detailed gene structure and alignment.
SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ...
doi:10.1093/nar/gkp982
pmid:19906715
pmcid:PMC2808913
fatcat:jygekcki6rh6pfhgowgexdeq74
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
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
2009
Nucleic Acids Research
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Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. ...
To organize the rapidly growing collection and enable systematic analyses, we created the Genomic tRNA Database (GtRNAdb), currently including over 74 000 tRNA genes predicted from 740 species. ...
Alternatively, tRNA genes can now be viewed within the eukaryotic-specific UCSC Genome Browser (5) or similar microbial genome browsers (6) . ...
doi:10.1093/nar/gkn787
pmid:18984615
pmcid:PMC2686519
fatcat:jirk2wc2mrbuhemvv4db736nom
Dr.VIS: a database of human disease-related viral integration sites
2011
Nucleic Acids Research
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Viral integration plays an important role in the development of malignant diseases. Viruses differ in preferred integration site and flanking sequence. ...
The authors also thank Dr Michael Galperin for the helpful suggestions. ...
The authors are grateful to Ms Xinyi Liu from Shanghai Jiao Tong University for comments on the earlier versions of the manuscript. ...
doi:10.1093/nar/gkr1142
pmid:22135288
pmcid:PMC3245036
fatcat:4bfrwwmfvndrzjx5y64ym76yla
IGVBrowser-a genomic variation resource from diverse Indian populations
2010
Database: The Journal of Biological Databases and Curation
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Acknowledgements The authors would like to thank Meenakshi Anurag, Pankaj Kumar for structuring the manuscript and Gajinder Pal Singh for correcting the draft and providing his valuable suggestions. ...
The web browser has been made dynamic for periodic future updates. ...
Database structure, implementation and accessibility The browser implements one of the widely used platformindependent genome annotation viewer Generic Genome Browser (GBrowse v1.69), developed by Stein ...
doi:10.1093/database/baq022
pmid:20843867
pmcid:PMC2942067
fatcat:keuqx6cjdjhwhnnkm2g64wr63y
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