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The UCSC Genome Browser Database: update 2009

R. M. Kuhn, D. Karolchik, A. S. Zweig, T. Wang, K. E. Smith, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, M. Pheasant, L. Meyer, F. Hsu (+10 others)
2009 Nucleic Acids Research  
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

B. Rhead, D. Karolchik, R. M. Kuhn, A. S. Hinrichs, A. S. Zweig, P. A. Fujita, M. Diekhans, K. E. Smith, K. R. Rosenbloom, B. J. Raney, A. Pohl, M. Pheasant (+11 others)
2009 Nucleic Acids Research  
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

P. A. Fujita, B. Rhead, A. S. Zweig, A. S. Hinrichs, D. Karolchik, M. S. Cline, M. Goldman, G. P. Barber, H. Clawson, A. Coelho, M. Diekhans, T. R. Dreszer (+15 others)
2010 Nucleic Acids Research  
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

K. R. Rosenbloom, T. R. Dreszer, J. C. Long, V. S. Malladi, C. A. Sloan, B. J. Raney, M. S. Cline, D. Karolchik, G. P. Barber, H. Clawson, M. Diekhans, P. A. Fujita (+15 others)
2011 Nucleic Acids Research  
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

Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, Janan T Eppig
2009 Nucleic Acids Research  
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

Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Takashi Gojobori, Tadashi Imanishi, Sumio Sugano
2009 Nucleic Acids Research  
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

G. L. Papadopoulos, M. Reczko, V. A. Simossis, P. Sethupathy, A. G. Hatzigeorgiou
2009 Nucleic Acids Research  
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

P. P. Gardner, J. Daub, J. G. Tate, E. P. Nawrocki, D. L. Kolbe, S. Lindgreen, A. C. Wilkinson, R. D. Finn, S. Griffiths-Jones, S. R. Eddy, A. Bateman
2009 Nucleic Acids Research  
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

T. Mituyama, K. Yamada, E. Hattori, H. Okida, Y. Ono, G. Terai, A. Yoshizawa, T. Komori, K. Asai
2009 Nucleic Acids Research  
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

Pora Kim, Suhyeon Yoon, Namshin Kim, Sanghyun Lee, Minjeong Ko, Haeseung Lee, Hyunjung Kang, Jaesang Kim, Sanghyuk Lee
2009 Nucleic Acids Research  
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

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

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

P. P. Chan, T. M. Lowe
2009 Nucleic Acids Research  
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

X. Zhao, Q. Liu, Q. Cai, Y. Li, C. Xu, Y. Li, Z. Li, X. Zhang
2011 Nucleic Acids Research  
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

A. Narang, R. D. Roy, A. Chaurasia, A. Mukhopadhyay, M. Mukerji, D. Dash
2010 Database: The Journal of Biological Databases and Curation  
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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