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TheSaccharomycesGenome Database Variant Viewer

Travis K. Sheppard, Benjamin C. Hitz, Stacia R. Engel, Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla S. Dalusag, Janos Demeter, Sage T. Hellerstedt, Kalpana Karra, Robert S. Nash (+5 others)
2015 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD; http: //www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation.  ...  Here we present the Variant Viewer: a dynamic opensource web application for the visualization of genomic and proteomic differences.  ...  the web.  ... 
doi:10.1093/nar/gkv1250 pmid:26578556 pmcid:PMC4702884 fatcat:ijhahwjuwrdspomzzmvqllpibu

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure

S. A. Chervitz, E. T. Hester, C. A. Ball, K. Dolinski, S. S. Dwight, M. A. Harris, G. Juvik, A. Malekian, S. Roberts, T. Roe, C. Scafe, M. Schroeder (+5 others)
1999 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD) collects and organizes information about the molecular biology and genetics of the yeast Saccharomyces cerevisiae.  ...  SGD can be accessed through the World Wide Web at http://genome-www. stanford.edu/Saccharomyces/  ...  INTRODUCTION The Saccharomyces Genome Database (SGD) exists to provide the scientific community with access to the Saccharomyces cerevisiae sequence and the wealth of associated information.  ... 
doi:10.1093/nar/27.1.74 pmid:9847146 pmcid:PMC148101 fatcat:mauijbflkzeaff67w4iegzs5j4

Integration of new alternative reference strain genome sequences into theSaccharomycesgenome database

Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla Dalusag, Janos Demeter, Stacia Engel, Sage T. Hellerstedt, Kalpana Karra, Benjamin C. Hitz, Robert S. Nash, Kelley Paskov (+5 others)
2016 Database: The Journal of Biological Databases and Curation  
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation.  ...  Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages.  ...  Variant Viewer can be use to visualize variation within AQY1 in the alternative strain genomes (Figure 4 ).  ... 
doi:10.1093/database/baw074 pmid:27252399 pmcid:PMC4888754 fatcat:wca5mblhhned7hid3dzbvxkzxi

Database resources of the National Center for Biotechnology Information

2019 Nucleic Acids Research  
Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST  ...  The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system.  ...  MegaBLAST is the default search program for NCBI's Genomic BLAST pages that search a set of genome-specific databases and generate, where possible, genomic views of the BLAST hits using the Map Viewer.  ... 
doi:10.1093/nar/gkz899 pmid:31602479 pmcid:PMC6943063 fatcat:coscu5vbd5gtnhii2uj7czx7au

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2000 Nucleic Acids Research  
ª 2005, the authors  ...  ; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its  ...  MegaBLAST is the default search program for NCBI's Genomic BLAST pages that search a set of genome-specific databases and generate, where possible, genomic views of the BLAST hits using the Map Viewer.  ... 
doi:10.1093/nar/28.1.10 pmid:10592169 pmcid:PMC102437 fatcat:xhsgpitasrd3na5mmjgz274zcq

SGD: Saccharomyces Genome Database

J. Cherry
1998 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the literature  ...  SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/  ...  SGD is supported by a P41, national resources, grant from the National Human Genome Research Institute at the US National Institutes of Health.  ... 
doi:10.1093/nar/26.1.73 pmid:9399804 pmcid:PMC147204 fatcat:s7efsm6vwvayhaoc7m3vjsfsbe

From one to many: expanding theSaccharomyces cerevisiaereference genome panel

Stacia R. Engel, Shuai Weng, Gail Binkley, Kelley Paskov, Giltae Song, J. Michael Cherry
2016 Database: The Journal of Biological Databases and Curation  
The Saccharomyces Genome Database (SGD) has long been the keeper of the original eukaryotic reference genome sequence, which was derived primarily from S. cerevisiae strain S288C.  ...  From one to many: expanding the Saccharomyces cerevisiae reference genome panel.  ...  the Variant Viewer, and are also available for download Table 5 ).  ... 
doi:10.1093/database/baw020 pmid:26989152 pmcid:PMC4795930 fatcat:p4oaxgtee5bybh73nmdvabyspe

GeneSeer: a sage for gene names and genomic resources

Andrew J Olson, Tim Tully, Ravi Sachidanandam
2005 BMC Genomics  
A variety of genomic data such as sequences, SNPs, splice variants, expression patterns and others can be accessed through the GeneSeer interface.  ...  A website http://geneseer.cshl.org/ is connected to the database to allow user-friendly access to our tools and external genomic resources using familiar gene names.  ...  The anonymous reviewers suggested several important improvements to the tool and the manuscript. One of the reviewers was instrumental in identifying competing tools.  ... 
doi:10.1186/1471-2164-6-134 pmid:16176584 pmcid:PMC1266031 fatcat:7g45z533kbfszpindtwxrgjbre

Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)

Sanjida H. Rangwala, Anatoliy Kuznetsov, Victor Ananiev, Andrea Asztalos, Evgeny Borodin, Vladislav Evgeniev, Victor Joukov, Vadim Lotov, Ravinder Pannu, Dmitry Rudnev, Andrew Shkeda, Eric M Weitz (+1 others)
2020 Genome Research  
NCBI's flagship genome browser, Genome Data Viewer (GDV), displays our in-house RefSeq annotation, is integrated with other NCBI resources such as Gene, dbGaP, and BLAST, and provides a platform for customized  ...  Here, we describe how members of the biomedical research community can use GDV and the related NCBI Sequence Viewer (SV) to access, analyze, and disseminate NCBI and custom biomedical sequence data.  ...  Acknowledgments We thank Arkadi Doubintchik for aid in project management and the NCBI QA team and Marina Omelchenko for testing of our graphical viewers.  ... 
doi:10.1101/gr.266932.120 pmid:33239395 pmcid:PMC7849379 fatcat:mx7haygquja3xhrdp2vntshl3q

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2006 Nucleic Acids Research  
In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and  ...  ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the National Institutes of Health. Conflict of interest statement. None declared.  ...  Saccharomyces Genome Database (SGD) (20) , Clusters of Orthologous Groups (COG) (15) and FlyBase.  ... 
doi:10.1093/nar/gkj158 pmid:16381840 pmcid:PMC1347520 fatcat:ajgh422s6nbi3o4beemsncsyzi

INTEGRATOR: interactive graphical search of large protein interactomes over the Web

Aaron N Chang, Jason McDermott, Zachary Frazier, Michal Guerquin, Ram Samudrala
2006 BMC Bioinformatics  
Integrator provides single and multiple protein searches of the Bioverse database containing experimentally-derived and predicted protein-protein interactions.  ...  We present Integrator, a web-integrated graphical search tool for protein-protein interaction networks across 50+ genomes.  ...  Integrator currently recognizes a number of identifiers including those from Genbank, Flybase, Wormbase, and the Saccharomyces Genome Database [10, [19] [20] [21] [22] [23] .  ... 
doi:10.1186/1471-2105-7-146 pmid:16542421 pmcid:PMC1459205 fatcat:uaed6t2sunep7hlyd4jnyfpfai

Database resources of the National Center for Biotechnology

D. L. Wheeler
2003 Nucleic Acids Research  
These pages search a set of genome-specific databases and generate, where possible, genomic views of the BLAST hits using the Map Viewer.  ...  NCBI has developed the Map Viewer for this purpose. Map Viewer The NCBI Map Viewer displays genome assemblies using sets of synchronized chromosomal maps.  ... 
doi:10.1093/nar/gkg033 pmid:12519941 pmcid:PMC165480 fatcat:dydxcilrszbt7g67rljindwu2a

Database resources of the National Center for Biotechnology Information

D. L. Wheeler
2001 Nucleic Acids Research  
ACKNOWLEDGEMENTS Funding to pay the Open Access publication charges for this article was provided by the National Institutes of Health. Conflict of interest statement. None declared.  ...  HomoloGene reports include homology and phenotype information drawn from OMIM, Mouse Genome Informatics (19) , Zebrafish Information Network (20) , Saccharomyces Genome Database (21), Clusters of Orthologous  ...  Genomic BLAST NCBI maintains Genomic BLAST pages for >45 organisms shown in the Map Viewer.  ... 
doi:10.1093/nar/29.1.11 pmid:11125038 pmcid:PMC29800 fatcat:mstubvho65h2noojeknidcplwi

Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa

Zilin Zhong, Min Yan, Wan Sun, Zehua Wu, Liyun Han, Zheng Zhou, Fang Zheng, Jianjun Chen
2016 Scientific Reports  
The Sanger sequencing was performed in probands of additional 95 Chinese ADRP families to investigate the contribution of PRPF3 to ADRP in Chinese population and another variant c.1532A > C (p.H511P) was  ...  These two variants, co-segregate with RP in two families respectively and both variants are predicted to be pathological.  ...  Acknowledgements The authors thank all patients and their family members for their participation. We also thank Dr. Cindy Yang and Dr. Jingbo Xiao for helpful comments.  ... 
doi:10.1038/srep37840 pmid:27886254 pmcid:PMC5122955 fatcat:o23mqgdzqrcxvld652doxk4ogy

Curated protein information in the Saccharomyces genome database

Sage T. Hellerstedt, Robert S. Nash, Shuai Weng, Kelley M. Paskov, Edith D. Wong, Kalpana Karra, Stacia R. Engel, J. Michael Cherry
2017 Database: The Journal of Biological Databases and Curation  
Due to recent advancements in the production of experimental proteomic data, the Saccharomyces genome database (SGD; www.yeastgenome.org) has been expanding our protein curation activities to make new  ...  These new data types have been included with the aim to facilitate cellular biology research.  ...  This work was supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health to the SGD project (U41 HG001315).  ... 
doi:10.1093/database/bax011 pmid:28365727 pmcid:PMC5467551 fatcat:newudxlhtvd5ljgb6lgppz4pp4
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