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PTM-Switchboard

http://cagr.pcbi.upenn.edu/PTMswitchboard/

Description :
Post-translational modifications of yeast transcription factors

The Cell Cycle DB

http://www.itb.cnr.it/cellcycle

Description :
Genes and proteins involved in human and yeast cell cycle

Open Proteomics Database

http://bioinformatics.icmb.utexas.edu/OPD/

Description :
Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium

StrainInfo.net Bioportal

http://www.straininfo.net/

Description :
The StrainInfo.net Bioportal currently integrates data from 55 Biological Resource Centres (BRCs) that cover all earth s continents and range from small niche-specific research collections to large general-purpose service collections into an integrated strain database that underpins the Bioportal (Dawyndt et al., 2005). Information extracted from three taxonomic reference databases together with their type strains is incorporated as well. This integration process has currently lumped over 690,000 strain numbers into about 310,000 equivalence classes that represent different strains of Bacteria, Archaea, filamentous fungi, yeasts, Algae and Protozoa. Through the online interface of the StrainInfo.net Bioportal, organisms can be searched by strain number, taxonomic name (optionally restricted to type strains of these species), INSDC accession number, full text or combinations of the previous search parameters. Query results redirect the user on-the-fly to the online catalogues of the different culture collections that have a given strain that matches the query in their holdings. Additional pointers allow the user to navigate the downstream information available on these organisms, thereby rendering superfluous the need to browse a multitude of autonomous and heterogeneous information sources. For each organism, a list of all sequences deposited in the INSDC databases is given as a separate view. This overview is dynamically compiled irrespective of the strain numbers assigned to different cultures of the same organism during the sequence deposition process, solving possible Babel-like confusions. Sequence records are linked out to the corresponding records in the INSDC databases and the SILVA database. Similarly, another view assembles all scientific publications on a given organism, with links to the PubMed and DOI repositories whenever available. Finally, the integrated history and geographic views allow simple inspection of strain authenticity and availability.

References :
Dawyndt, P., Vancanneyt, M., De Meyer, H., Swings, J. (2005) Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Transactions on Knowledge and Data Engineering, 17(8), pp. 1111-1126.

GeneDB

http://www.genedb.org/

Description :
The GeneDB projects primary goal is to develop and maintain curated database resources for three organisms: Schizosaccharomyces pombe, the kinetoplastid protozoa Leishmania major, and Trypanosoma brucei.

AHMII

http://www.wdcm.org/AHMII/ahmii.html

Description :
Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

Virtual Library--Yeast

http://genome-www.stanford.edu/Saccharomyces/VL-yeast.html

Description :
Links to yeast resources.

Yeast Resource Center

http://depts.washington.edu/~yeastrc/index.html

Description :
Provides expertise and access through collaboration to mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction; very good info on each of the techniques.

S. pombe genome

http://www.sanger.ac.uk/Projects/S_pombe/

Description :
Schizosaccharomyces pombe Genome Sequencing Project.

SCMD

http://scmd.gi.k.u-tokyo.ac.jp/

Description :
The Sacharomyces Cerevisiae Morphological Database (SCMD) is a collection of micrographs of budding yeast mutants; visualization and data mining tools are provided.

RF_DYMHC

http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htm

Description :
RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.

YMF 3.0

http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.pl

Description :
YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.

YOGY

http://www.sanger.ac.uk/PostGenomics/S_pombe/YOGY/

Description :
Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also beretrieved.

BioGRID

http://www.thebiogrid.org/

Description :
Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at http://www.thebiogrid.org. BioGRID release version 2.0 includes more than 116,000 interactions from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. An internally hyper-linked web interface allows for rapid search and retrieval of interaction data. Full or user-defined datasets are freely downloadable as tab-delimited text files and PSI-MI XML. Pre-computed graphical layouts of interactions are available in a variety of file formats. User-customized graphs with embedded protein, gene and interaction attributes can be constructed with a visualization system called Osprey that is dynamically linked to the BioGRID.

Recent develoments :
Over 30,000 protein and genetic interactions have recently been added from 5,778 sources through exhaustive curation of the S. cerevisiae primary literature (Reguly et al, submitted). An analogous systematically curated set of interactions compiled from the Schizosaccharomyces pombe (fission yeast) literature will also be deposited shortly. Selected physical interaction datasets for TGF-b, TOR and cancer networks in mammalian cells will also be deposited in the near future. A new quantitative genetic interaction experimental descriptor has been added to accommodate recent Epistatic Mini-Array Profiles (E-MAP) and other forms of quantitative genetic interaction data generated in S. cerevisiae.

Gene Aging Nexus

http://gan.usc.edu/

Description :
Gene Aging Nexus (GAN, http://gan.usc.edu) is a data mining platform for the biogerontological-geriatric research community. It enables users to analyze, query, and visualize the aging-related genomic data. Our goal is to facilitate the digestion and usage of the public genomic data. A current focus is on integrative analysis of microarray gene expression data. We are establishing a central database for aging microarray data of six species: human (H. sapiens), rat (R. norvegicus), mouse (M. musculus), fruit fly (D. melanogaster), worm (C. elegans), and yeast (S. cerevisiae). GAN is equipped with a set of bioinformatics tools for analysis of the microarray data sets, cross-platform and cross-species.

Aknowledgement :
The work was supported by a pilot grant from the Seaver foundation, the NIH Grants R01GM074163, P50HG002790, P01AG14751, R01AG13499, and the NSF grant 0515936

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