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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.  ...  The latest protein structure and comparison tools available at SGD are presented here.  ...  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

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 Model Organism BLASTP Best Hits resource displays, for each S.cerevisiae protein, the single most similar protein from several model organisms and presents links to the database pages of those proteins  ...  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 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

Expanded protein information at SGD: new pages and proteome browser

R. Nash, S. Weng, B. Hitz, R. Balakrishnan, K. R. Christie, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman, E. L. Hong, M. S. Livstone (+13 others)
2007 Nucleic Acids Research  
the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) to enhance the depth and accessibility of protein annotations.  ...  This Proteome Browser has enabled SGD to unify the display of hidden Markov model (HMM) domains, protein family HMMs, motifs, transmembrane regions, signal peptides, hydropathy plots and profile hits using  ...  Funding to pay the Open Access publication charges for this article was provided by National Human Genome Research Institute.  ... 
doi:10.1093/nar/gkl931 pmid:17142221 pmcid:PMC1669759 fatcat:mooxlzramva7roidk5mxc53kd4

Association rule mining of gene ontology annotation terms for SGD

Anurag Nagar, Michael Hahsler, Hisham Al-Mubaid
2015 2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)  
In this work, we present a technique to find association relationships in the annotation terms for the Saccharomyces cerevisiae (SGD) genome.  ...  The presented method has a number of advantages -it relies only on the structure of the gene ontology, has minimal memory and storage requirements, and can be easily scaled for large genomes, such as the  ...  The Gene Ontology Consortium manages the annotations for various species in specific databases such as the Saccharomyces cerevisiae database, or the Homo sapiens database [2] .  ... 
doi:10.1109/cibcb.2015.7300289 dblp:conf/cibcb/NagarHA15 fatcat:3qdgp2nzyjebffgxymonp7amou

Gene Ontology annotations at SGD: new data sources and annotation methods

E. L. Hong, R. Balakrishnan, Q. Dong, K. R. Christie, J. Park, G. Binkley, M. C. Costanzo, S. S. Dwight, S. R. Engel, D. G. Fisk, J. E. Hirschman, B. C. Hitz (+12 others)
2007 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD; http:// www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae  ...  Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods.  ...  Funding to pay the Open Access publication charges for this article was provided by the National Human Genome Research Institute.  ... 
doi:10.1093/nar/gkm909 pmid:17982175 pmcid:PMC2238894 fatcat:kwe3m5tfdnehnctlg3ueguw2ca

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  
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  ...  work in classifying the literature and their assistance in defining the workflow for the Genome Map data sets.  ...  Introduction Since its inception in 1993, Saccharomyces Genome Database (SGD) (1) has been dedicated to annotating and characterizing the budding yeast genome, serving as a comprehensive resource for  ... 
doi:10.1093/database/bar057 pmid:22434826 pmcid:PMC3308148 fatcat:wwzz7etezvho3hd4fpbe4b44ia

A New Path Length Measure Based on GO for Gene Similarity with Evaluation using SGD Pathways

Anurag Nagar, Hisham Al-Mubaid
2008 2008 21st IEEE International Symposium on Computer-Based Medical Systems  
For validation purposes, we computed the similarity of genes from the Saccharomyces Genome Database (SGD) taking part in various cellular pathways.  ...  The measure uses only one feature (path length) for computing the similarity between genes.  ...  The GO project is collaboration between 35 model organism databases; among them FlyBase (Drosophila melanogaster), SGD (Saccharomyces Genome Database) and MGD (Mouse Genome Database) were the first group  ... 
doi:10.1109/cbms.2008.27 dblp:conf/cbms/NagarA08 fatcat:5ksoi276pjdezjzfxz2bpooh4q

Expanding yeast knowledge online

Kara Dolinski, Catherine A. Ball, Stephen A. Chervitz, Selina S. Dwight, Midori A. Harris, Shannon Roberts, Taiyun Roe, J. Michael Cherry, David Botstein
1998 Yeast  
INTRODUCTION There are now three major Saccharomyces databases that maintain web servers: Saccharomyces Genome Database (SGD), Munich Information Center for Protein Sequences (MIPS) and Yeast Protein Database  ...  Researchers may also view the results of S. cerevisiae chromosome-bychromosome comparisons using the Genome-wide DNA Similarity View and protein-by-protein comparisons using the Genome-wide Protein Similarity  ... 
doi:10.1002/(sici)1097-0061(199812)14:16<1453::aid-yea348>3.0.co;2-g pmid:9885151 pmcid:PMC3037831 fatcat:ml4b6vbignb7hhu3ct5wq3nhni

TheSaccharomycesGenome Database: A Tool for Discovery

J. Michael Cherry
2015 Cold Spring Harbor Protocols  
The Saccharomyces Genome Database (SGD) is the main community repository of information for the budding yeast, Saccharomyces cerevisiae.  ...  This database is the Saccharomyces Genome Database (SGD; www.yeastgenome.org; Cherry et al. 2012).  ...  ACKNOWLEDGMENTS I am grateful to all the present and past staff of the Saccharomyces Genome Database project for their dedication to accuracy and their service to life science educators and researchers  ... 
doi:10.1101/pdb.top083840 pmid:26631132 pmcid:PMC5673599 fatcat:ihqfz63o35e2dmqh6fpt4kr73a

Yeast Protein Database (YPD): a database for the complete proteome of Saccharomyces cerevisiae

W. E. Payne, J. I. Garrels
1997 Nucleic Acids Research  
The Yeast Protein Database (YPD) is a database for the proteins of the budding yeast, Saccharomyces cerevisiae. YPD is the first annotated database for the complete proteome of any organism.  ...  Now that the complete genome sequence of yeast is available, YPD contains entries for each of the characterized proteins and for each of the uncharacterized proteins predicted from the sequence.  ...  We also thank Mike Cherry and the staff at SGD for updates and corrections to YPD. Finally we thank all those who participated in the yeast genome project for making this resource possible.  ... 
doi:10.1093/nar/25.1.57 pmid:9016505 pmcid:PMC146399 fatcat:gon2wfzr25cjpp57xfzbwc7gsi

Integrating functional genomic information into the Saccharomyces Genome Database

C. A. Ball
2000 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome.  ...  The SGD is accessible via the WWW at http://genome-www. stanford. edu/Saccharomyces/ GENERAL FORMAT OF SGD's NEW LOCUS PAGE  ...  The diverse information in the Saccharomyces Genome Database (SGD) is organized around individual genes.  ... 
doi:10.1093/nar/28.1.77 pmid:10592186 pmcid:PMC102447 fatcat:jb4l3fqgcfdo5gl3lzjj77pade

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  ...  Most importantly, the SGD project would not be possible without the continued communication and support of the worldwide community of yeast researchers who provide suggestions for improvement and notice  ... 
doi:10.1093/nar/gkr1029 pmid:22110037 pmcid:PMC3245034 fatcat:y7wg4tq63fhtvk4vq4z6nlfrmi

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.  ...  ACKNOWLEDGEMENTS We thank the P-POD team at Princeton University for their generous sharing of their data with us. We thank the yeast research community for their input and support.  ... 
doi:10.1093/nar/gkx1112 pmid:29140510 pmcid:PMC5753351 fatcat:bzd2jvlocnbqpbczmgoofs3tmi
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