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Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

K. R. Christie
2004 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD; http:// www.yeastgenome.org/), a scienti®c database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several new  ...  The Fungal Alignment Viewer displays alignments of sequences from multiple fungal genomes, while the Sequence Similarity Query tool displays PSI-BLAST alignments of each S.cerevisiae protein with similar  ...  INTRODUCTION The Saccharomyces Genome Database (SGD) collects and organizes biological information about genes and proteins of the yeast Saccharomyces cerevisiae from the scienti®c literature, and presents  ... 
doi:10.1093/nar/gkh033 pmid:14681421 pmcid:PMC308767 fatcat:sgjwrwxhc5clhk3avtgtlxl55u

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 aids researchers by providing not only basic information, but also tools such as sequence similarity searching that lead to detailed information about features of the genome and relationships between  ...  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

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)

R. Balakrishnan
2004 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD; http:// www.yeastgenome.org/) is a scientific database of gene, protein and genomic information for the yeast Saccharomyces cerevisiae.  ...  The Fungal BLAST tool provides directed searches against all fungal nucleotide and protein sequences available from GenBank, divided into categories according to organism, status of completeness and annotation  ...  INTRODUCTION The Saccharomyces Genome Database (SGD) collects and organizes biological information about genes and proteins of Saccharomyces cerevisiae, and presents this information on individual Locus  ... 
doi:10.1093/nar/gki023 pmid:15608219 pmcid:PMC539977 fatcat:w4oavqa6yfhljfrqwdtv4nqh3u

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

S. S. Dwight
2002 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over the  ...  made between gene products, both within Saccharomyces cerevisiae and across species.  ...  The availability of published experimental data for Saccharomyces cerevisiae as a model organism, and the participation of other organism databases (currently Drosophila melanogaster, Mus musculus, Arabidopsis  ... 
doi:10.1093/nar/30.1.69 pmid:11752257 pmcid:PMC99086 fatcat:g4s4vniso5fk5nlofa3zahyifa

Saccharomyces Genome Database: the genomics resource of budding yeast

J. M. Cherry, E. L. Hong, C. Amundsen, R. Balakrishnan, G. Binkley, E. T. Chan, K. R. Christie, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman (+10 others)
2011 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD, http:// www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae.  ...  The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions  ...  of issues in the data and tools the authors provide.  ... 
doi:10.1093/nar/gkr1029 pmid:22110037 pmcid:PMC3245034 fatcat:y7wg4tq63fhtvk4vq4z6nlfrmi

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

Stacia R. Engel, J. Michael Cherry
2013 Database: The Journal of Biological Databases and Curation  
(Fritz) Roth for early access to the BY4741 and BY4742 genome sequences; Gail Binkley and Edith D.  ...  Hitz for incorporation and analyses of strain genomes; Markus Ralser for early access to the W303 genome sequence; Takafumi Yamaguchi and Frederick P.  ...  the Saccharomyces Genome Database (SGD).  ... 
doi:10.1093/database/bat012 pmid:23487186 pmcid:PMC3595989 fatcat:gs6uhkli6re2fiw55flt42qd7m

Saccharomyces genome database informs human biology

Marek S Skrzypek, Robert S Nash, Edith D Wong, Kevin A MacPherson, Sage T Hellerstedt, Stacia R Engel, Kalpana Karra, Shuai Weng, Travis K Sheppard, Gail Binkley, Matt Simison, Stuart R Miyasato (+1 others)
2017 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD; http: //www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae  ...  These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute or the National Institutes of Health.  ... 
doi:10.1093/nar/gkx1112 pmid:29140510 pmcid:PMC5753351 fatcat:bzd2jvlocnbqpbczmgoofs3tmi

Saccharomyces Genome Database provides mutant phenotype data

S. R. Engel, R. Balakrishnan, G. Binkley, K. R. Christie, M. C. Costanzo, S. S. Dwight, D. G. Fisk, J. E. Hirschman, B. C. Hitz, E. L. Hong, C. J. Krieger, M. S. Livstone (+10 others)
2009 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD; http:// www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's  ...  The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary  ...  ACKNOWLEDGEMENTS The image used in Figure 1 is from Ohkuni et al. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkp917 pmid:19906697 pmcid:PMC2808950 fatcat:eigs74zk4fdffeu3lljuede4oy

New mutant phenotype data curation system in the Saccharomyces Genome Database

M. C. Costanzo, M. S. Skrzypek, R. Nash, E. Wong, G. Binkley, S. R. Engel, B. Hitz, E. L. Hong, J. M. Cherry
2009 Database: The Journal of Biological Databases and Curation  
Acknowledgements We thank members of SGD's Scientific Advisory Board and our Stanford colleagues, in particular Gavin Sherlock and Jared Wenger, for helpful comments during the development of the curation  ...  Collecting and organizing this range of phenotypic data is among the most important missions of the Saccharomyces Genome Database (SGD; www. yeastgenome.org).  ...  SGD provides comprehensive information about the yeast genome, including the complete genomic sequence as well as the biological roles of chromosomal features and gene products, all curated from the scientific  ... 
doi:10.1093/database/bap001 pmid:20157474 pmcid:PMC2790299 fatcat:qg6x4lnyezhuln26xhdkp4e3ym

The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes

Sudheer Tumu, Ashish Patil, William Towns, Madhu Dyavaiah, Thomas J. Begley
2012 Database: The Journal of Biological Databases and Curation  
Our resulting database provides a mineable list of multi-codon data and can be used to identify unique sequence runs and codon usage patterns in individual and functionally linked groups of genes.  ...  5780 Saccharomyces cerevisiae genes.  ...  Supplementary data Supplementary data are available at Database Online. Funding Funding for open access charge: National Institutes of Health (ES01225101 and ES015037 to T.J.B.); James D.  ... 
doi:10.1093/database/bas002 pmid:22323063 pmcid:PMC3275765 fatcat:v4urki6n3nbdriu2oi2gue4eiu

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report

E. T. Chan, J. M. Cherry
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We thank Edith Wong and Benjamin Hitz for their assistance in track setup and GBrowse configuration; Gail Binkley and Stuart Miyasato for adding the Genome Map data files to the downloads  ...  server; Dianna Fisk for assistance in defining dataset metadata; Craig Amundsen for aid with the UCSC liftOver tool; Shuai Weng and Kalpana Karra for helpful discussions and the SGD biocurators for their  ...  Since its inception, SGD has become the authority on the Saccharomyces cerevisiae genome sequence, gene names and annotation.  ... 
doi:10.1093/database/bar057 pmid:22434826 pmcid:PMC3308148 fatcat:wwzz7etezvho3hd4fpbe4b44ia

Biocuration at theSaccharomycesgenome database

Marek S. Skrzypek, Robert S. Nash
2015 Genesis  
Saccharomyces Genome Database is an online resource dedicated to managing information about the biology and genetics of the model organism, yeast (Saccharomyces cerevisiae).  ...  This system provides a foundation for further analysis of experimental data coming from research on yeast as well as other organisms.  ...  and improving SGD.  ... 
doi:10.1002/dvg.22862 pmid:25997651 pmcid:PMC4545726 fatcat:krnxivky4fdvviye4bunx2dz7m

PartCrafter: Find, Generate, and Analyze BioParts

Emily Scher, Shay B Cohen, Guido Sanguinetti
2019 Synthetic Biology  
We present PartCrafter, a tool which extracts and aggregates genomic feature data in order to facilitate the search for new BioParts with specific functionalities.  ...  While there are a number of software tools which allow users to design complex DNA sequences by stitching together BioParts or genetic features into genetic devices, there is a lack of tools assisting  ...  Joel Bader, the Rosser Lab at the University of Edinburgh, and Jordan Matelsky for helpful discussions which improved this application.  ... 
doi:10.1093/synbio/ysz014 pmid:32995539 pmcid:PMC7445878 fatcat:eb4xa65l6re6jen7bp4tfnik5a

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

D. O. Inglis, M. B. Arnaud, J. Binkley, P. Shah, M. S. Skrzypek, F. Wymore, G. Binkley, S. R. Miyasato, M. Simison, G. Sherlock
2011 Nucleic Acids Research  
The Candida Genome Database (CGD, http://www .candidagenome.org/) is an internet-based resource that provides centralized access to genomic sequence data and manually curated functional information about  ...  As the scope of Candida research, and the number of sequenced strains and related species, has grown in recent years, the need for expanded genomic resources has also grown.  ...  ACKNOWLEDGEMENTS The authors would like to thank Ge´nolevures for making the C. glabrata CBS138 sequence available, Brendan Cormack and Suzanne Noble for strain lineage information, and Mike Cherry and  ... 
doi:10.1093/nar/gkr945 pmid:22064862 pmcid:PMC3245171 fatcat:qfogwktijnbufkeevqgqiey5ka

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

Devin R. Scannell, Oliver A. Zill, Antonis Rokas, Celia Payen, Maitreya J. Dunham, Michael B. Eisen, Jasper Rine, Mark Johnston, Chris Todd Hittinger
2011 G3: Genes, Genomes, Genetics  
describe their comparison to the genomes of S. cerevisiae and S. paradoxus.  ...  These nearly complete genome sequences and the collection of genetically marked strains provide a valuable toolset for comparative studies of gene function, metabolism, and evolution, and render Saccharomyces  ...  2002; Cliften et al. 2003; Dujon et al. 2004; Kellis et al. 2004; Souciet et al. 2009 ), the NCBI nr protein database, and S. cerevisiae Ty and LTR sequences downloaded from Saccharomyces Genome Database  ... 
doi:10.1534/g3.111.000273 pmid:22384314 pmcid:PMC3276118 fatcat:s2xlrpat6bggbczjbiiq4dqmu4
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