Bioinformatics and Functional Genomics

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Chapter 15: Completed genomes: Fungi


Web resources from Chapter 15
Website URL
The Museum of Paleontology at the University of California, Berkeley http://www.ucmp.berkeley.edu/fungi/fungi.html
The American Museum of Natural History (New York) http://ology.amnh.org/biodiversity/treeoflife/pages/fungi.html
Fungal infections on the Apollo missions http://lsda.jsc.nasa.gov/scripts/cf/exper.cfm?exp_index=372
MIPS map of chromosome XII http://mips.gsf.de/proj/yeast/CYGD/db/index.html
The Saccharomyces Genome Database http://genome-www.stanford.edu/Saccharomyces/MAP/GENOMICVIEW/GenomicView.html
S. cerevisiae chromosome matrix generator http://acer.gen.tcd.ie/~khwolfe/yeast/
The Génolevures project http://cbi.labri.fr/Genolevures/
SGD http://genome-www.stanford.edu/Saccharomyces/
MIPS http://mips.gsf.de/genre/proj/yeast/index.jsp
The TRIPLES database

http://ygac.med.yale.edu/triples/triples.htm

A. fumigatus genome http://www.tigr.org/tdb/e2k1/afu1/
The Aspergillus Web Site http://www.aspergillus.man.ac.uk/
The Candida albicans genome http://sequence-www.stanford.edu/group/candida/index.html
Neurospora crassa genome database at the University of New Mexico http://biology.unm.edu/biology/ngp/home.html
Neurospora crassa genome database at the Whitehead Institute http://www-genome.wi.mit.edu/annotation/fungi/neurospora/
Neurospora crassa genome database http://www.mips.biochem.mpg.de/proj/neurospora/
The P. chrysosporium genome sequencing project http://www.jgi.doe.gov/programs/whiterot.htm
S. pombe genome sequence analysis http://www.sanger.ac.uk/Projects/S_pombe/
The Schizosaccharomyces Gene Index http://www.tigr.org/tdb/spgi/
Virtual Library: Yeast http://genome-www.stanford.edu/Saccharomyces/VL-yeast.html
Glossary of yeast terms http://www.phys.ksu.edu/gene/gloss.html

 

Tables

Table 15-7. Yeast expression data available on the web (from the MIPS database, ( http://mips.gsf.de/proj/yeast/CYGD/db/index.html), November 2002).
Subject Reference
Metabolic shift from fermentation to respiration DeRisi et al. (1997)
Sporulation Chu et al. (1998)
Cell cycle Spellman et al. (1998)
Transcription Holstege et al. (1998)
Response to alkylating agent Jelinsky and Samson (1999)
Multidrug resistance DeRisi et al. (2000)
Microarray global viewer Marc et al. (2001)

Table 15-8. Fungal genome sequencing projects (from NCBI). Abbreviations: Chr, chromosome number; Mb, megabase pairs; NA, not available.

Organism Size Chr URL/Reference
Aspergillus fumigatus 30 Mb 8 http://www.sanger.ac.uk/Projects/A_fumigatus/
http://bioinf.man.ac.uk/
http://www.pasteur.fr/externe
http://www.tigr.org/
Aspergillus nidulans 28.5 Mb 8 http://www.cereon.com/
Aspergillus parasiticus NA NA http://www.genome.ou.edu/fungal.html
Candida albicans 16 Mb 8 http://sequence-www.stanford.edu/group/candida/index.html
Cryptococcus neoformans 21 Mb NA http://rcweb.bcgsc.bc.ca/cgi-bin/cryptococcus/cn.pl
http://www.nagasaki-u.ac.jp/english/index.html
http://www-sequence.stanford.edu/group/C.neoformans/index.html
http://www.genome.ou.edu/cneo.html
Fusarium sporotrichioides NA NA http://www.genome.ou.edu/fsporo.html
Magnaporthe grisea 40 Mb 7 http://www.wi.mit.edu/
http://www.fungalgenomics.ncsu.edu/index.htm
Neurospora crassa 43 Mb 7 http://www-genome.wi.mit.edu/
http://biology.unm.edu/biology/ngp/home.html
http://www.genome.ou.edu/fungal.html
Phanerochaete chrysosporium 30 Mb 10 http://www.jgi.doe.gov/programs/whiterot.htm
Saccharomyces cerevisiae 12 Mb 16 http://genome-www.stanford.edu/Saccharomyces/
Schizosaccharomyces pombe 13.8 Mb 3 Nature 415:871-880, 2002
Ustilago maydis 20 Mb   NA LION Bioscience and Bayer

 

Web resources

Description
The SGD
Virtual Library: Yeast
Glossary of yeast terms
S. pombe genome sequencing project
Aspergillus genomics
Candida albicans-Stanford Genome Technology Center
Candida albicans information
Fungal genome resource Home
S. cerevisiae promoter database
Tools for regulatory sequence analysis
AdvancedQuery.html SAGE advanced query
Yeast SAGE
EUROFAN projects
Yale genome analysis center
Cell cycle analysis project
Pat Brown Lab
Genome-Wide Expression Page
Transcriptional program of sporulation
Fungal genetics stock center
Yeast virtual library
Biosci
Munich information center for protein sequences home
mips-yeast genome
AMPhora Expression Data Analysis
Saccharomyces genome database
Mitochondrial biogenesis database


 

 

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