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Database which provides annotated sequence data for the genomes of basidio and ascomycete yeasts. The resources provided include genetic element pages, data sets for downloading, quick and advanced searches, facilities for BLAST comparisons, and a genome browser powered by JBrowse from GMOD.
Proper citation: Genome Resources for Yeast Chromosomes (RRID:SCR_015005) Copy
http://www-sequence.stanford.edu/group/yeast_deletion_project/
Database and project to reveal open reading frames (ORFs) in the yeast genome in order to discover their functions. A PCR-based gene deletion strategy is used to assign functions through phenotypic analysis of mutants.
Proper citation: Saccharomyces Genome Deletion Project (RRID:SCR_014961) Copy
Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GeneCodis (RRID:SCR_006943) Copy
http://www.oeb.harvard.edu/faculty/hartl/old_site/lab/publications/GeneMerge.html
THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: GeneMerge (RRID:SCR_005744) Copy
A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.
Proper citation: Synapse (RRID:SCR_006307) Copy
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