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About AspGD
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Genome Snapshot,
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This is the home of the Aspergillus
Genome Database, 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.
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AspGD News
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AspGD Protein Information Pages now available
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AspGD has expanded to include protein information for all verified
and predicted ORFs. Using software and database tools developed at the
Saccharomyces Genome Database (SGD),
the Protein Information Pages display basic property, domain organization,
structural and homology information. To view the page for a given protein,
navigate to the Locus Summary page for the corresponding gene and click on the
"Protein" tab towards the top of the page.
Example Protein Pages:
VeA;
BenA;
An8399.
(Posted February 5, 2010)
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Aspergillus fumigatus Genome Browser now available in AspGD
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The genome of Aspergillus fumigatus strain Af293 may now be explored using the GBrowse Genome Browser at AspGD. 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. The tool may be accessed from the "A. fumigatus GBrowse" link on the menu located on the left-hand side of the AspGD home page. GBrowse allows you to zoom in or out on any genomic region or navigate to a different region of the chromosome, display restriction sites or G-C content, view DNA or protein sequence, or take advantage of additional browser features, which are described on the GBrowse Help Documentation page. Please note that you may need to select "Reset" (located under the search examples) to display all of the options the first time you view A. fumigatus GBrowse. The GBrowse software was written by Lincoln Stein as part of the Generic Model Organism Database (GMOD) Project.
(Posted January 26, 2010)
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AspGD Curation News
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Pseudogenes and Untranslated Regions in AspGD
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We have added the pseudogenes and untranslated regions (UTRs) from version 4 of the A. nidulans annotation (the Eurofungbase annotation) to AspGD. The Advanced Search tool can be used to search and retrieve lists of pseudogenes and features with annotated UTR regions.
(Posted December 16, 2009)
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Updated Gene Ontology terms and orthology mappings for Aspergillus nidulans genes
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We have updated the sets of orthology mappings and predicted molecular function, biological process, and cellular location Gene Ontology annotations for A. nidulans genes. These assignments are based on the latest annotation at AspGD and at the Saccharomyces Genome Database (SGD).
The orthology mappings between A. nidulans and S. cerevisiae were made using the Inparanoid software developed at the Karolinska Institutet. In cases where an A. nidulans gene has an S. cerevisiae ortholog for which SGD has assigned GO terms, and these GO assignments meet our criteria (described in more detail in the associated README file), these GO terms are assigned to the A. nidulans gene with the evidence code "IEA" (Inferred from Electronic Annotation), which indicates that these annotations are predicted computationally, with no curatorial review. Downloadable files containing the orthology mappings and GO annotations are available. Based on orthology, we have inferred 13202 GO annotations for 3314 A. nidulans genes in AspGD.
(Posted December 3, 2009)
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Aspergillus Genomic Online Community group
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The Aspergillus Genomic Online Community is a new group
available to members of the worldwide community of Aspergillus researchers.
The group is hosted by the Aspergillus Website,
an information resource for Aspergillus and Aspergillosis. (Posted October 20, 2009)
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AspGD paper in Nucleic Acids Research Database Issue
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A paper entitled "The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community" will appear in the 2010 Database Issue of Nucleic Acids Research. The paper is now available online as a Nucleic Acids Research Advance Access article.
(Posted October 7, 2009)
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Orthologs and syntenic regions
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AspGD users can now navigate from A. nidulans genes to orthologs and syntenic regions in the other sequenced Aspergillus species. Links are
available from the Locus Summary page that navigate to an interactive comparative visualization tool (see example). Alternatively, the
ortholog clusters can be searched for gene name from any Aspergillus
species, at http://aspgd.igs.umaryland.edu/.
Orthologs among the sequenced Aspergillus
genomes were generated via a modified mutual best hit (MBH) approach, in which close paralogs are collapsed into a single node prior to MBH clustering.
AspGD is using Sybil, an open source, web-based software package for searching and visualizing the comparative genome data (http://sybil.sf.net). (Posted October 2, 2009)
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Aspergillus nidulans annotation update
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The Broad Institute has released a reannotation of the Aspergillus nidulans genome sequence generated by an improved automated annotation pipeline. It is currently available on their website and is expected to appear in Genbank soon. AspGD is working to merge this annotation with the curated subset of the current annotation and we will post an update when the new release is available.
The previously published Eurofungbase reannotation of the Aspergillus nidulans genome (Wortman et al., 2009), the result of a community curation effort, is now available as Third Party Annotation (TPA) at Genbank through the efforts of the CADRE database. (Posted September 29, 2009)
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Predicted Gene Ontology terms and orthology mappings for Aspergillus fumigatus genes
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We have generated orthology mappings between A. nidulans and A. fumigatus, and between S. cerevisiae and A. fumigatus, using the Inparanoid software developed at the Karolinska Institutet. The ortholog mapping files are available for download from our website.
We have also made Gene Ontology term predictions for A. fumigatus genes based on orthology to A. nidulans and S. cerevisiae. A file containing these predictions is also available for download from our website. In cases where an A. fumigatus gene has an A. nidulans ortholog for which
we have GO terms in AspGD, or an S. cerevisiae ortholog for which the Saccharomyces Genome Database has assigned GO terms, and these GO assignments meet our criteria (described in more detail in the associated README file), these terms are assigned
to the A. fumigatus gene with the evidence code "IEA" (Inferred from Electronic
Annotation), which indicates that these annotations are predicted computationally,
with no curatorial review. (Posted September 25, 2009)
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A. nidulans tRNA genes added to AspGD
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We have now added tRNA-encoding genes to AspGD. These genes were predicted using the tRNAscan-SE algorithm developed by T. M. Lowe and S. R. Eddy. The names appear in the following format: a lower-case t (for "tRNA"), followed by the one-letter abbreviation of the amino acid with which it is charged, followed by the anticodon (in parenthesis) followed by an integer. For example, "tA(AGC)1" is an alanyl tRNA with an AGC anticodon.
The tRNAscan-SE algorithm predicts that there are 175 tRNA genes in the A. nidulans genome. The algorithm also predictes 5 pseudo-tRNA genes and they are noted as 'pseudogene' in the AspGD database. To find all of the tRNAs in AspGD, please use the Advanced Search tool or the following wildcard query for Quick Search: t*(*)*
These tRNA genes also appear in the GBrowse genome browser.
(Posted August 26, 2009)
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Announcing the Aspergillus Genome Database
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We are pleased to announce that AspGD
is now available. The menu on
the left-hand side of this page
provides links to search options,
tools, and additional information.
AspGD currently contains Locus Summary pages for 10,545
Aspergillus nidulans protein-coding genes that represent the
most current sequence annotation, incorporating the original
annotation from the Broad Institute, the re-annotation at TIGR, and
the Eurofungbase community annotation effort. We have added 2,180 Gene
Ontology (GO) term assignments for 968 genes, derived from the
community curation effort involving Eurofungbase in conjunction with
TIGR/JCVI and Aspergillus research laboratories. We have also
predicted orthology to S. cerevisiae genes, using InParanoid, and have assigned
9,923 GO terms for 2,442 genes based on the current GO annotation of
experimentally characterized S. cerevisiae orthologs in the
Saccharomyces Genome Database (SGD). More than 1,400
publications have been added to AspGD and linked to the Literature
Guides for the genes mentioned in their abstracts. Please note that
because this initial reference load was based on automated PubMed
searches, reference lists will be incomplete, and irrelevant
references may be present. Going forward, references will be manually
screened to ensure that each gene has a complete and accurate
reference list.
Literature curation will be a major focus at AspGD in the coming
months as we work towards comprehensive curation of gene function,
localization, and mutant phenotype information from the
A. nidulans literature. As an illustration of a manually curated Locus
Summary page, we have collected and curated literature relevant to the
veA gene.
Initially, we are concentrating on curation of A. nidulans,
because it serves as a genetic model for the other Aspergilli, and it
is the most well-represented of these species in the published
experimental literature. In the future, we will add sequences from
other Aspergillus species to AspGD and employ an optimized
annotation pipeline across all genomes to maintain a set of current
and consistent gene boundary annotations and link between genomes
based on orthology and synteny data.
We welcome your comments and suggestions. Please feel free to contact us and let us know how we can
better serve the Aspergillus research community.
(Posted March 13, 2009)
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AspGD at the 25th Fungal Genetics Conference
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We have submitted the following abstract to the 25th Fungal Genetics
Conference, which will take place in March, 2009:
The Aspergillus Genome Database (AspGD), a curated database of Aspergillus gene, protein, and genomic sequence information for the fungal research community.
Martha Arnaud1, Gail Binkley1, Marcus Chibucos2, Maria Costanzo1, Jonathan Crabtree2, Stuart Miyasato1, Prachi Shah1, Marek Skrzypek1, Jennifer Russo Wortman2, and Gavin Sherlock1
1Department of Genetics, Stanford University, Stanford, CA 94305-5120
2Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
We have recently obtained funding to create a resource for the Aspergillus research community, AspGD, which will be a multispecies genomics database modeled on the Candida and Saccharyomyces Genome Databases. Our goal is to facilitate research on Aspergilli and on other medically and economically important fungal pathogens by providing a first-stop reference for Aspergillus genomics and molecular biology, with up-to-date, high-quality, curated scientific information and web-based research tools. We will implement an optimized annotation pipeline across all Aspergillus genomes, to maintain a set of current and consistent gene boundary annotations, and will incorporate links between genomes based on orthology and synteny data. Gene function, localization, and mutant phenotype annotations will be manually curated from the Aspergillus literature. We will provide web-based tools for sequence visualization and retrieval, and for analysis of sequence information and gene product annotations. All of the data in AspGD will be freely available to the public from http://www.aspgd.org/. In addition, we will maintain a colleague registry by which Aspergillus research community members may share contact information and research interests, to facilitate collaboration. We strive to be responsive to the needs of the research community, and we welcome your feedback and suggestions.
AspGD curators may be reached by email at aspergillus-curator@genome.stanford.edu
AspGD is supported by grant RO1 AI077599 from the NIAID at the NIH.
We hope to see you there!
(Posted February 25, 2009)
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Previous news items are available from the AspGD News Archive
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Note: The
Aspergillus Genome Database provides
information about the molecular biology of Aspergillus to
researchers. AspGD staff are not physicians and
cannot give medical advice. Information about
pathogenic fungal infections can be found online in the PubMed
database or at Medline
Plus page at the US National Institutes of
Health web site.
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