Project background perhaps no other fungal genus contains species that are so harmful and species that are so beneficial to humans as the genus aspergillus 1, and a large number of aspergillus species are of biomedical and industrial significance. Please note that downloading primary data and analysis results from our broad institute gdac firehose constitutes an acknowledgement that you and collaborators will. Annotated genomes allomyces macrogynus aspergillus comparative site aspergillus nidulans aspergillus terreus batrachochytrium dendrobatidis blastomyces dermatitidis er3 slh14081 atcc. New resources for functional analysis of omics data for. We also use trnascan software to generate consistent catalogs of trna. The gbrowse genome browser is a tool for viewing and navigation of genomic sequence, developed as part of the generic model organism database project. Over 100 fungi have been sequenced, including human and plant pathogens as well as fungi that serve as basic models for molecular and cellular biology. If you have a question, see the faq or the user guide. Download data files are described in detail in their associated readme documents. Annotated genomes allomyces macrogynus aspergillus comparative site aspergillus nidulans aspergillus terreus batrachochytrium dendrobatidis blastomyces. New resources for functional analysis of omics data for the genus. The broad institute hosts an internal genepattern server, available only to broad institute members and collaborators. The fungal genomics group at the broad institute has sequenced and analyzed a wide diversity of fungal organisms that are important to medicine, agriculture and industry.
Here we report the genome sequence of the model organism aspergillus nidulans, and a comparative study with aspergillus fumigatus, a serious human pathogen, and aspergillus. Project background perhaps no other fungal genus contains species that are so harmful and species that are so beneficial to humans as the genus aspergillus. The aspergillus genome database aspgd is a unique webbased resource. She obtained an msc degree in molecular, cellular and genetic biotechnology from the university of cordoba, spain, in 2012, and in bioinformatic and computational biology from the institute. The aspergillus genome database aspgd is an online genomics resource. Aspergillus genome database, a curated comparative. Project background perhaps no other fungal genus contains species that are so harmful and species that are so beneficial to humans as the genus aspergillus 1, and a large number of aspergillus species. Aspgd contains information about genes and proteins of multiple aspergillus species. See the section on loading genomes for instructions hosted assemblies. Mochiview motif analysis and genome browser software posted april 22.
The eupathdb family of databases supports a wide range of microbial eukaryotes, including protozoan parasites and many fungal and oomycete species. Leland stanford junior university, and broad institute. Genepattern provides hundreds of analytical tools for the analysis of gene expression rnaseq and microarray, sequence variation and copy number, proteomic, flow cytometry, and network analysis. To cite your use of the molecular signatures database msigdb, a joint project of uc san diego and broad institute, please reference subramanian, tamayo, et al. Database with genomic information on the fungal pathogen aspergillus. Broad institute is a missiondriven community that brings together researchers in medicine, biology, chemistry, computation, engineering, and mathematics from across mit, harvard, and. Aspgds mission is to serve the scientific research community by improving the structural and functional annotation associated with the aspergillus. Aspergillus community news aspergillus genome database. Genome sequence, annotation, and tools at the broad institute. Aspergillus genome database, a curated comparative genomics. Annotated genomes allomyces macrogynus aspergillus comparative site aspergillus nidulans aspergillus terreus batrachochytrium dendrobatidis blastomyces dermatitidis er3 slh14081 atcc 18188 atcc 26199 botrytis cinerea candida comparative site candida albicans wo1 candida guilliermondii candida lusitaniae candida tropicalis chaetomium globosum coccidioides immitis h538. Broad institute of mit and harvard is empowering a revolution in biomedicine to accelerate the pace at which the world conquers disease. The choice of enzyme determines via its pam requirements which ontarget sites are considered. All of the features outlined above for the public broad hosted server are available with.
Vcf stands for variant call format, and it is used by the genomes project to encode structural genetic variants. The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Genome database sgd, which allowed us to make these changes efficiently, with maximal reuse of existing software. If you are new to gsea, see the tutorial for a brief overview of the software. Broad global health initiative, broad technology labs, food allergy science. We have iteratively improved the structural annotation of aspergillus genomes through the analysis of publicly available transcription data, mostly expressed sequenced tags, as described in a previous nar database article arnaud et al. To cite your use of the gsea software, a joint project of uc san diego and broad institute, please reference subramanian, tamayo, et al. The genus aspergillus comprises fungal species that are important model.
Target tumor alterations relevant for genomicsdriven therapy is a database of genes that, when somatically altered in cancer, are directly linked to a clinical action. Furthermore, offtarget cfd scores are reduced for sites that depart from this pam. See viewing variants for example igv visualizations of mutation and vcf files. Each gene was represented by 10 oligonucleotide probe pairs 24.
Cadre aspergillus metabolic pathway database view and search metabolic pathways for several aspergillus species, provided by cadre and the aspergillus website. We have made significant updates to the structural annotation of the aspergillus fumigatus af293 reference genome based on pasa analysis using rnaseq data from muller et al. The institute is independently governed and supported as a 501c3 nonprofit research organization under the name broad institute inc. Postgenomics approaches in fungal research briefings.
Miyasato sr, binkley j, orvis j, shah p, wymore f, sherlock g, wortman jr 20. The aspergillus fumigatus af293 genome was sequenced by jcvi, the sanger institute, and the institut pasteur, and the sequence and annotation were downloaded from the broad institute aspergillus download page. Pasa update made in 2011, incorporating ests strain a1560 and cdss. The aspergillus genome database aspgd is an online genomics resource for researchers studying the genetics and molecular biology of the aspergilli. Pathways were predicted using pathway tools software. This helps us track and better serve our user community. Developed in the data sciences platform at the broad institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Transcriptional profiles of smooth muscle biopsies of diabetic and normal individuals. The fungal genomics group at the broad institute has sequenced and analyzed a wide diversity of fungal organisms that are important to medicine, agriculture.