SGD

SGD Site Map

Contents:

Overview

The SGD site map provides a comprehensive listing of major SGD resources and tools. It is organized by the major categories available at SGD, which correspond to the links located on the left side of the home page. The resources and tools available in that category are listed, followed by a description of the resource and its primary use. A link to the help documentation is also provided, if it is available for that resource.

For more information on how to navigate around SGD, please read the Getting Started page.

Site map

Category Resource Description Primary Use Help Page
Search Options Basic Search Restrict searches of the SGD relational database to specific criteria, such as literature guide, colleague information, protein information, and text. Search SGD database using keywords. help page
Advanced Search Find a chromosomal feature (e.g. gene, ORF, centromere) based on selected criteria (e.g. calculated pI, MW, chromosome number, GO-Slim terms, etc.) Find chromosomal features that match specific properties or annotations. help page
Full-text literature search (Textpresso) SGD Literature Search powered by Textpresso, a text-mining tool useful for the extraction of user specified information from full-text journal articles Find journal articles that contain keywords or keywords in combination with specific categories help page
Search SGD Web Pages Search SGD HTML pages, excludes the relational database. Find SGD web pages using keywords located on the page.  
Global Gene Hunter Simultaneous retrieval of information for a given locus from the following seven databases:
(1)SGD (2)Genbank (3)PubMed (4)PDB Homolog (5)Swiss-Prot (6)Comprehensive Yeast Genome Database (MIPS) (7) Protein Information Resource (PIR)		 Find information on one gene from many databases. help page
Table of Gene Summary Paragraphs A list of genes that have a written synopsis of published information, including selected references, written in natural language by SGD Scientific Curators. Find an overview and key references for a gene.  
List of genome-wide analysis papers Link to a list of genome-wide analysis papers (eg. microarrays analysis publications) curated at SGD. Find SGD curated papers that analyze the entire genome. help page
YGM Meeting Abstracts
2006 | 2004 | 2002 | 2000 | 1998 | 1996		 Search Yeast Genetics & Molecular Biology Meeting abstracts. Find an abstract from the YGMB meeting.  
International YGM Meeting Abstracts
2005 | 2003 | 2001		 Search International Yeast Genetics & Molecular Biology Meeting abstracts. Find an abstract from the International YGMB meeting.  
Category Resource Description Primary Use Help Page
Help Resources Getting Started Common uses of SGD for the first time user. Get a brief overview of navigating around SGD.  
FAQ Answers to some of the most common questions asked by SGD users. Get an answer to a commonly asked question.  
General Yeast Topics Describes the yeast model organisms: Saccharomyces cerevisiae (budding yeast), Schizosaccharomyces pombe (fission yeast), and Candida albicans. Find information about common yeast species.  
What's New in SGD Changes and additions to SGD resources. Find new resources at SGD and when they were added.  
Glossary SGD terms and definitions. Find the definition of a new term.  
Category Resource Description Primary Use Help Page
Analysis & Tools BLAST Search S. cerevisiae DNA and protein sequence datasets for similarities to a particular sequence. Find similarities between a sequence of interest and S. cerevisiae DNA or protein sequences. help page
FASTA Search S. cerevisiae DNA and protein sequence datasets for similarities to a particular sequence. Uses a different algorithm than BLAST and can produce a different result. Find similarities between a sequence of interest and S. cerevisiae DNA or protein sequences. help page
Gene/Sequence Resources Retrieve S. cerevisiae genomic sequence from SGD or paste in a DNA or protein sequence to analyze it using numerous SGD resources. Display and analyze an S. cerevisiae sequence (or other sequence) in many ways. help page
Pattern Matching A pattern matching program that allows ambiguous matches but not gaps. Find short DNA/protein sequence matches in S. cerevisiae. help page
Design Primers Recommends primers appropriate for either PCR or sequencing of a given gene or DNA sequence, within parameters set by the user (end points, Tm, GC/AT ratios, etc.). Design sequencing and PCR primers for S. cerevisiae. help page
Genome Restriction Analysis Generates a restriction map of a specified DNA sequence. The restriction map may include all enzymes, or a subset of enzyme types (3' overhangs, 5' overhangs, blunt ends, or enzymes that cut once or twice). Display the restriction map for a S. cerevisiae sequence. help page
Vectordb Collected sequences of cloning vectors for use in a variety of organisms including (but not limited to) S. cerevisiae, Drosophila, C. elegans, and Phage. Find descriptions and sequence of vectors  
Genomic View Whole genome graphic of S. cerevisiae with the ability to view a narrow region. Displays include DNA sequence Features, Physical Map, and Physical and Genetic Maps. View centromeres and select marker genes on all 16 chromosomes of S. cerevisiae with links to each chromosome. help page
Physical & Genetic Maps Combined physical and genetic map for each chromosome of S. cerevisiae. Overview an entire chromosome, comparing mapping and sequencing data, of S. cerevisiae. help page
Fungal BLAST Search multiple fungal genomes for similarity to a particular sequence Find similarities between a sequence of interest and fungal nucleotide or protein sequences. help page
Category Resource Description Primary Use Help Page
Homology & Comparisons PSI-BLAST Results Find the results for an S. cerevisiae protein that was used as the query sequence for PSI-BLAST analysis against UniProt's UniRef90 protein dataset Find proteins in other species that contain sequence similarity to the S. cerevisiae protein. help page
Fungal Alignment Viewer View ClustalW alignments of S. cerevisiae protein or nucleotide sequences with those of other fungi. Allows you to generate custom alignments by choosing the species to include and the type of sequence to align. Compare S. cerevisiae protein, gene, and flanking region sequences to similar sequences from other fungi. help page
PDB Homolog Query This query page allows you to search for structural information on S. cerevisiae proteins by gene name, keyword, PDB identifier, or chromosome. Find structural information on S. cerevisiae and similar proteins. help page
Yeast Protein Motif Query This query page allows you to retrieve motif information for an S. cerevisiae protein. Also displays what other S. cerevisiae proteins share the motifs. Find motifs in S. cerevisiae proteins. help page
Synteny Viewer Genome wide alignments between S. cerevisiae, S. paradoxus, S. mikatae, and S. bayanus. This is pre-publication data that is part of a larger work by Manolis Kamvysselis, Nick Patterson, Eric Lander, and others at the Whitehead Institute for Biomedical Research. Find orthologs of your favorite gene in other Saccharomyces species. help page
Category Resource Description Primary Use Help Page
Function & Expression
Expanded Phenotype Search Search the text of all phenotype information to find phenotypes of interest and view the genes associated with them. Search for a common yeast phenotype (such as petite), an allele (such as act1-1), or an experimental condition (such as MMS). help page
Search Interactions View physical and genetic interactions for a gene. Find curated physical and genetic interactions with references for a gene. help page
Yeast Biochemical Pathways View and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Search for and view a biochemical pathway, a reaction using the EC number, and chemical compounds. help page
Protein Page Provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Find basic information about a S. cerevisiae protein. help page
Expression Connection Simultaneous retrieval of S. cerevisiae gene expression data for a given locus from a large number of published experiments, see the list at the URL above. Retrieve gene expression data from multiple microarray experiments. help page
Webminer Queries gene expression datasets on an experiment by experiment basis. In addition to microarray data, Webminer includes a variety of information about every ORF in the yeast genome including its promoter sequence, the protein sequence, and the molecular weight, allowing users to generate complex queries of the microarray data. Retreive gene expression data on an experiment by experiment basis help page
Category Resource Description Primary Use Help Page
GO Resources What is GO? SGD help page that explains the philosophy of GO. Get an overview of Gene Ontology (GO).  
GO Tutorial SGD tutorial that highlights pages and tools that use GO annotations to familiarize users with the Gene Ontology (GO). Learn where GO annotations are located on SGD pages.  
GO-Slim Term Mapper GO-Slim is a set of GO terms that represent major sections of the ontology. Gene products are annotated to the most specific GO term possibile. This tool traces the specific annotations to a GO-Slim term that is shared by a group of S. cerevisiae genes. Find the GO-slim term to which a set of S. cerevisiae genes is annotated. help page
GO Term Finder An S. cerevisiae gene product is annotated to the most specific GO term possible. Common parent terms may not be obvious. This tool determines the GO terms that a set of S. cerevisiae genes shares in common and graphically displays the significant lineage. Finds GO terms that are shared by a group of S. cerevisiae genes. help page
Category Resource Description Primary Use Help Page
Community Info Yeast Laboratories Links to PIs of yeast laboratories who have submitted colleague information to SGD. Find a PI (principal investigator) of a yeast laboratory.  
Biosci Yeast Archives Search the Yeast Biosci Newsgroup. Find messages posted to the newsgroup based on a keyword.  
Conferences & Courses Link to a list of conferences & courses. Find an upcoming conference.  
External Links List of useful external sites Find a web site for information not available at SGD.  
Category Resource Description Primary Use Help Page
Submit Data Gene Registry Form to register a gene name. Register a gene name at SGD.  
About the gene registry Description and history of the SGD gene registry. Learn about the history of the SGD gene registry.  
Gene Naming Guidelines Guidelines to registering a gene name as agreed upon by the members of the yeast community. Find information and guidelines to registering a gene name and determining when the gene name becomes a standard name.  
Colleague Submission/Update Form Form to submit colleague information to SGD. Your information will be available to the yeast community. Add or update your information in SGD. help page
Contact SGD Form to submit suggestions or questions to SGD. Send suggestions or questions to SGD.  
Category Resource Description Primary Use Help Page
Download Data Download Data files from SGD Download sequence, tables, and other yeast data. Each directory contains a README that describes the files' contents and format. The downloads page contains a description of all the data directories. Download tab-delimited files of information from SGD. help page
Batch Download Tool that allows simultaneous retrieval of DNA sequences, protein sequences, and chromosomal coordinate information for a list of Standard gene names or Feature names. Download information for a list of genes from SGD. help page
Download SGD Lite Download and install SGD Lite, a lightweight version of SGD in a freely available database system (PostgreSQL). Install information at SGD on your personal machine. help page
Gene Name Lists Lists of SGD gene names in various formats. Download lists of SGD gene names in various formats.  
Codon Usage Tables Codon frequencies were calculated using known or predicted ORFs. Available as a downloadable table. Find codon frequencies for the S. cerevisiae genome.  
Commonly Used Auxotrophic Markers Lists of information about several commonly used alleles Find basic information on a commonly used allele.  
Meoitic Double-Strand Breaks on Chromosome III Graphic and tabular views of the data of A. Nicolas and F. Baudat(Proc. Natl. Acad. Sci. USA 94:5213-5218) View location of double-strand breaks in chromosome III.  
Yeast Images A gallery of yeast pictures contributed by members of the yeast community View and download images of yeast.  
SGD ORF Additions based on SAGE Tabular list of the 27 new ORFS added by SGD based on its analysis of the SAGE data of Velculesu, et al., (1997) Cell 88:243-251 Find ORFs that were added to SGD based on SAGE.  
Systematic Sequencing Table Information about the S. cerevisiae systematic sequencing effort. Find links to download S. cerevisiae chromosomal sequences and contact information. help page
Table of Updates to the Systematic Sequencing List of changes made to the systematic sequence Find ORFs that were added or deleted since the systematic sequencing effort.  
Category Resource Description Primary Use Help Page
About SGD About SGD About the SGD project. Find out background information on the SGD project.  
Citing SGD How to cite SGD in publications. References to use in citing SGD.  
Staff Names and addresses and SGD staff. Find out who works at SGD.  
WWW Usage Weekly SGD usage statistics Find statistics on SGD usage.  
Documentation Information about SGD's Oracle database, including schema & table specification Find techical history and details about the SGD database.  
SGD Publications
2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 		SGD Articles in the database issue of Nucleic Acids Research Download and read SGD publications in NAR.  

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