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     YEASTS & other FUNGI
 

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Saccharomyces cerevisiae

Databases/searches

  • General:
    • SGD  Saccharomyces Genome Database is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae
    • YPD  Yeast Protein Database  from Proteome
    • MYGD, the MIPS Yeast Genome Database presents a comprehensive database which summarizes the current knowledge regarding the more than 6000 ORFs encoded by the Yeast Genome.
    • S. cerevisiae Sequencing Project at Sanger Centre
    • S. cerevisiae complete genome: RefSeq from NCBI
    • GeneQuiz of Saccharomyces cerevisiae genome
    • Webminer, "a database of databases used to study gene expression patterns in yeast. All the information in webminer is freely available elsewhere. Webminer makes it easy to perform sophisticated searches by organizing some of the vast wealth of published genomic data under one roof. "
    • Yeast PEDANT (Protein Extraction, Description, and ANalysis Tool) is a software system that utilizes modern bioinformatics methods to provide complete functional and structural characterization of protein sequence sets - from individual sequences to complete genomes.
    • Yeast Chromosome Sequences The files are in Genbank format. 
    • Yeast Protein Function Assignment Project
    • YPM Yeast Protein Map: 2D Gel Map of Saccharomyces cerevisiae proteins
    • XREFdb Cross-referencing Yeast and Human Genes
  • Specialized:
    • TRIPLES  a database of TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces. 
    • snoRNA Database -- Small Nucleolar RNAs from the Yeast Saccharomyces cerevisiae
    • YIDB  The Yeast Intron DataBase contains currently available information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae. 
    • MitBASE A database on nuclear genes involved in mitochondrial biogenesis and its regulation
    • YTPdb Yeast Transport Protein database provides free access to the data of a whole genomic scale analysis of the membrane transport proteins of the yeast Saccharomyces cerevisiae. The last release of YTPdb contains a total of 216 proteins (excluding mitochondrial carriers and multi subunit H+ ATPases). Roughly two thirds of these proteins were discovered by genome sequencing and are still of unknown physiological function.
    • PathCalling A Database of results from two large-scale yeast two-hybrid screens for identification of protein-protein interactions between full-length open reading frames predicted from the Saccharomyces cerevisiae genome sequence. DB presents 957 putative interactions involving 1,004 S. cerevisiae proteins. 
    • SCPD The Promoter Database of Saccharomyces cerevisiae
    • Yeast Gene Duplications This Web site contains data on duplicated genes in the yeast (Saccharomyces cerevisiae) genome. It concentrates particularly on duplicated chromosomal regions. 
    • Yeast Cell Cycle Analysis Project. The goal of this project is to identify all genes whose mRNA levels are regulated by the cell cycle.
     
Schizosaccharomyces pombe
 
Candida albicans
 
Neurospora crassa, Aspergillus sp., and other  fungi
  • MNCDB -- MIPS Neurospora crassa database
  • Neurospora Genetic Nomenclature, Fungal Genetics Newsletter 46:31-41
  • Fungal  Cosmid and cDNA Sequencing (Aspergillus nidulans, Aspergillus parasiticus and Neurospora crassa)
  • NGP  Neurospora Genome Project at the University of New Mexico
  • Stocks
    • FGSC  Fungal Genetics Stock Center (Allomyces, Ascobolus, Aspergillus, Blastocladiella, Coniochaeta, Fusarium, Gelasinospora, Nectria, Neurospora, Podospora, Sordaria)
  • FGR Fungal Genome Resource (Aspergillus nidulans, Neurospora crassa, Nectria haematococca, Pneumocystis carinii)
  • Aspergillus web site  This site is designed to provide information on pathogenic Aspergilli for clinicians and scientific researchers. The site includes DNA sequence data, a comprehensive bibliographic database, laboratory protocols, treatment information and discussion groups. There is also a seperate section devoted to the needs of people who suffer from the various effects of Aspergillus ( the 'Aspergillus for patients' website) 
  • Aspergillus nidulans Linkage Map, Linkage Data, Maps, Locus Lists, Strainlist and Annual Bibliographies
  • Aspergillus-Genomics.org -- Maps, sequences, etc.
  • Zoosporic Fungi  The goal of this site is to provide a web-based resource of information on zoosporic fungi, an informal group which includes chytrids, oomycetes, labyrinthulids, and various other protists
  • Chytridiales  Chytrid Fungi Online. Here you will find information on members of the order Chytridiales in the phylum Chytridiomycota (Kingdom Fungi), including a description of genera, tips and techniques on how to isolate chytrids, current hypotheses of chytrid phylogeny, links to other relevant websites, and a searchable reference database
  • PcWeb Pneumocystis Genome Project and Resource Site
  • Phycomyces web site
 
General Resources

Portals

Nomenclature and Taxonomy Stocks, Mutants, and Reagents
  • YGSC Yeast Genetic Stock Center at ATCC
  • SDP the Saccharomyces Deletion Project 
  • Fungi and Yeasts Collection at ATCC
  • CABRI Common Access to Biological Resources and Information. The centres taking part in this project currently hold 26 collections covering most of the biodiversity: human and animal cells, bacteria, fungi, yeasts, plasmids, animal and plant viruses, DNA probes. The total holdings of their collections are nearly 140,000 deposits (90,000 of which are currently included in the catalogues), which represent approximately half of available deposits in Europe. 
  • FGSC  Fungal Genetics Stock Center (Allomyces, Ascobolus, Aspergillus, Blastocladiella, Coniochaeta, Fusarium, Gelasinospora, Nectria, Neurospora, Podospora, Sordaria)
Maps


Methods and Protocols


Societies and Meetings


Newsgroups


Labs and People


Literature

Intoductory and Educational Resources


Medicine

  • Medical Mycology  This web site is devoted to medically important fungi and the health related problems caused by them
  • Aspergillus web site  This site is designed to provide information on pathogenic Aspergilli for clinicians and scientific researchers. The site includes DNA sequence data, a comprehensive bibliographic database, laboratory protocols, treatment information and discussion groups. There is also a seperate section devoted to the needs of people who suffer from the various effects of Aspergillus ( the 'Aspergillus for patients' website) 
Organelles
  • FMGP  Fungal Mitochondrial Genome Project. The goals of FMGP are to (i) sequence complete mitochondrial genomes from all major fungal lineages, (ii) infer a robust fungal phylogeny, (iii) define the origin of the fungi, their protistan ancestors, and their specific phylogenetic link to the animals, (iv) investigate mitochondrial gene expression, introns, RNAse P RNA structures, mobile elements ...
 
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