Aspergillus Genomics - Fungal Genome Links

The Aspergillus Genome Database.
This is a resource for genomic sequence data and gene and protein information for Aspergilli. AspGD is based on the Candida Genome Database and is funded by the National Institute of Allergy and Infectious Diseases at the US National Institutes of Health.

 

BLAST with fungal genomes at NCBI.
A facility to search against the genomic sequences of various fungi, including Aspergillus fumigatus, A. nidulans and A. terreus. Searching against protein sequences is also provided for some species, including A. nidulans.

 

MycoPathPD at Incyte Genomics.
MycopathPD, a database of protein information for the major fungal pathogens of humans is available by paid subscription only. The following species have been annotated : Aspergillus flavus, A. fumigatus, A. niger, Blastomyces dermatidis, Candida albicans, C. dubliniensis, C. glabrata, C. guillermondii, C. krusei, C. lusitaniae, C. parapsilosis, C. pseudotropicalis, C. tropicalis, Coccidioides immitis, Cryptococcus neoformans, Histoplasma capsulatum, Pneumocystis carinii.

 

Fungal Cosmid and cDNA Sequencing at Oklahoma University (Bruce Roe)

This site contains the sequence of cosmids from Aspergillus nidulans, A. parasiticus and Neurospora crassa. It contains A. nidulans and N. crassa EST databases which are searchable using Blast.

 

Database of Genomes and Transcriptional Regulation for Filamentous Fungi at the NIBH, Japan (Masayuki Machida)

This site contains the Aspergillus oryzae EST database and the sequence of a single A. nidulans cosmid SW06H01.

Other fungal genome links (excluding S. cerevisiae)

Fungal Genome Resource at the University of Georgia (Jonathon Arnold)

This site contains physical maps of Aspergillus nidulans, Neurospora crassa, Nectria haematococca and Pneumocystis carinii. It contains databases of N. crassa and P. carinii cosmid end sequence and P. carinii ESTs which are searchable using Blast.

 

Neurospora crassa Database at the Whitehead Institute Center for Genomic Research (Bruce Birren and Chad Nusbaum)

This site contains the third release of the 10 x whole genome shotgun (February 12, 2002: Assembly of 821 contigs >2kb containing 38,044,343 base pairs) which can be downloaded or searched using Blast.

 

MIPS Neurospora crassa database (Ulrich Schulte)

This site describes the sequencing of linkage groups II and V. The sequences are searchable using Blast and detailed annotations of over 1300 ORFs are available as well an automatic annotation of almost 3000 ORFs, a view of the contigs and a list of the clones.

 

Neurospora Genome Project at the University of New Mexico (Mary Anne Nelson)

The Neurospora Genome Project (NGP) represents an effort to obtain partial or complete nucleotide sequences from a large number of cDNA clones derived from conidial, mycelial, unfertilized sexual and perithecial libraries of N. crassa. A collaboration with the University of Georgia is underway to develop a detailed physical map of the N. crassa genome. A Blast server for the Neurospora ESTs is available. All of the Neurospora ESTs that show significant identity to proteins that have been sequenced in other organisms have been categorised in a proteome database according to a slightly modified version of the EGAD scheme.

 

TIGR Neurospora crassa Gene Index

The TIGR N. crassa Gene Index integrates research data from international N. crassa EST sequencing and gene research projects. The goal of the project is to represent a non-redundant view of all N. crassa genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.

 

Fungal Genomics Laboratory at North Carolina State University (Ralph Dean)

This site describes the projects being carried out in this laboratory. The main purpose of the lab is to study the rice blast fungus, Magnaporthe grisea. Major funding has been obtained to sequence chromosome 7 and provide 35,000 EST's. Other projects include work on the genomes of Aspergillus niger, A. flavus and Trichoderma reesei.

 

RiceBlastDB at the University of Cornell (Immanuel Yap).

RiceBlastDB is a database that aims to integrate the diverse types of information being generated about Magnaporthe Grisea, the causal agent of rice blast disease. It contains genetic and physical maps, marker data, population structure, DNA fingerprints, pathotype, mating type, and geographical distribution. The database also includes an extensive bibliography as well as contact information for colleagues who are working on different aspects of the fungus and the disease.

Candida DB at the Pasteur Institute (Christophe d'Enfert)
The genomics database for Candida albicans that has been made public by the European Consortium Galar Fungail and is based on an annotation of Assembly 6 of the C. albicans genome sequence produced at the Stanford Genome Technology Center. Alternate database location.

Saccharomyces Genome DB is hosting a web page where news, updates, etc. about the annotation of the Candida genome will be posted.

Sequencing of Candida albicans at Stanford University (Ron Davis)

The Stanford DNA Sequencing and Technology Center has been whole genome shotgun sequencing strain SC5314 of Candida albicans up to a coverage of 10X, performing as much assembly of the sequence as possible, using recognizable genes as nucleation points. The sequence is searchable by Blast.

Candida albicans information at the University of Minnesota (Stewart Scherer and Pete Magee)

The Candida albicans information pages support our efforts to build a complete physical map of the chromosomes. The site provides the means to rapidly distribute to the Candida research community recent data from the project and other information about Candida molecular genetics. The C. albicans information exists in two major sections: an information page primarily for active researchers in the field (strains, DNA probes, unpublished mapping and sequence data) and a genetics page organized more like a review article (integrating data from the current research activities with extensive tables and references to the literature). Both sections contain pages about comparison of the Candida data with information from S. cerevisiae.

 

Pilot project: Candida albicans at the Sanger Institute (Marie-Adele Rajandream)

The Sanger Centre is carrying out a pilot sequencing project on the Candida albicans strain 1161 genome in collaboration with Prof. Duncan Shaw at the University of Aberdeen. A set of 10 cosmids is being sequenced for this pilot project.

 

Cryptococcus neoformans Genome Project at the Stanford Genome Technology Center (Richard Hyman)

The goal of this project is to produce the sequence of the genome of the fungus Cryptococcus neoformans (strain JEC 21, also known as B-4500, serotype D). In particular, to maximize sequence data while minimizing time and money, a whole genome shotgun has been undertaken. The random shotgun reads have been assembled into contigs and open reading frames identified.

 

The Schizosaccharomyces pombe Genome Sequencing Project at the Sanger Institute (Valerie Wood)

 

Pneumocystis Genome Project and Resource Site at the University of Kentucky (Chuck Staben)

 

Pneumocystis carinii Telomeric Clone Sequencing at the Sanger Institute (Neil Hall)

Beowulf Genomics has funded the Sanger Centre to sequence 10 cosmid clones. Of these, 2 cosmids will contain telomeric DNA and 8 sub-telomeric DNA.

Trichoderma reesei EST Database at the University of Sao Paulo (Hamza El-Dorry)

Fungal Genome Databases at the Human Genome Mapping Project

Directory of yeast and other fungal websites

 

Fungal Mitochondrial Genome Project (FMGP) at the University of Montreal (B. Franz Lang)

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.

General genome links

Nature & Nature Genetics Genome Gateway

Welcome to Nature's Genome Gateway, a comprehensive web resource devoted to genomics. Access is free.

 

The Sanger Institute

 

The Institute for Genomic Research

 

National Center for Biotechnology Information

 

European Bioinformatics Institute

 

The Whitehead Institute for Biomedical Research / MIT Center for Genome Research

 

Codon Usage Tabulated from GenBank at the Kazusa DNA Research Institute, Chiba, Japan

 

Ribosomal Database Project at Michigan State University

The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences.

 

Incyte Genomics, Inc.

 

Millennium Pharmaceuticals, Inc.

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