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AspGD News Archive

2013 AspGD News Archive

 

Sequence trace files available

We have added archival Aspergillus sequence data from the NCBI TraceDB site, and these data are now available from our AspGD download site. (Posted November 8, 2013)

New "Big 4" ortholog alignment

We have added a new, streamlined, four-species protein alignment to the ortholog cluster pages in our Sybil Comparative Genomics Viewer. This "Big 4" alignment displays a Clustal protein alignment of the orthologs from A. nidulans FGSC A4, A. oryzae RIB40, A. fumigatus Af293 and A. niger CBS513.88 (see example). As we continue to add new species into our Sybil Comparative Genomics Viewer, the number of proteins represented in each multispecies ortholog cluster has grown significantly. We continue to provide an alignment of all of the orthologs from the full set of species, and now include the "Big 4" alignment in addition. We hope this feature is helpful, and we welcome your feedback any time. (Posted August 13, 2013)

A. niger annotation updates

The A. niger reference gene set has been updated, based on PASA analysis. 4,123 features were affected: 543 CDSs were extended and 195 shortened; 30 features were merged into 15 features; 2,907 5-prime UTRs and 2,601 3-prime UTRs were added or modified; New exons were added to the ends of 270 features, and the internal intron/exon structure was modified for 491 features. The GBrowse Genome Browser displays the old annotation as a "Historic Track" to facilitate visual comparison, for example, of new UTRs or gene model structure updates, for example, a gene merge. The current and historic reference annotation can be viewed alongside RNA-Seq transcript data in AspGD JBrowse (zoom in to see spliced reads across intronic regions, including the intron within what was previously annotated as an intergenic region). (Posted August 13, 2013)

Introducing JBrowse for AspGD

JBrowse is now available for exploring large-scale data in AspGD, including RNA-Seq data for A. nidulans FGSC A4, RNA-Seq and genomic variation data for A. fumigatus Af293, and RNA-Seq data for A. niger CBS 513.88 and A. oryzae RIB40. To see the large-scale data in the region of any gene, select the JBrowse link on the Locus Summary page, for example, in the "RNA-Seq Data" section of the A. nidulans veA page. The JBrowse software has been developed as part of the GMOD project.

The links to the GenomeView browser are no longer displayed on the Locus Summary pages due to incompatibilities of the browser software software with some web browsers and versions of Java. Genome View may still be accessed from the Search Options page. (Posted June 19, 2013)

RNA-Seq data used to improve reference annotation for A. fumigatus

We have made significant updates to the structural annotation of the Aspergillus fumigatus Af293 reference genome based on PASA analysis using RNA-Seq data (from Müller et al. [2012]) to provide experimental support for gene model modifications. The coordinates of 5,174 features were updated: 1,044 CDSs were extended and 641 shortened; 28 features were merged into 14 features; 4,524 5-prime UTRs and 3,545 3-prime UTRs were added or modified; New exons were added to the ends of 1,255 features, and the internal intron/exon structure was modified for 1,133 features.

In addition, we have updated the structural annotation of the Aspergillus fumigatus A1163 (CEA10) strain, which is not the reference strain, but for which we provide sequence files, protein domain files, and mulispecies BLAST capabilities. The PASA analysis of A. fumigatus A1163 utilized RNA-Seq data provided by JCVI (SRA project SRP003796). (Posted April 2, 2013)

Additions and Improvements to Datasets Available for Download and BLAST at AspGD

We are happy to announce six new Aspergillus genomes available to search with the AspGD BLAST tool:
  • A. acidus
  • A. aculeatus ATCC16872
  • A. brasiliensis
  • A. carbonarius ITEM 5010
  • A. sydowii
  • A. versicolor
All six strains were sequenced by JGI. Sequence and annotation for these strains are available for download from the JGI site, subject to their terms of usage policy.

AspGD has added protein domain predictions for six additional Aspergillus strains:
  • A. clavatus NRRL 1
  • A. flavus NRRL 3357
  • A. fumigatus A1163
  • A. niger ATCC 1015
  • A. terreus NIH2624
  • N. fischeri NRRL 181
Domain predictions were made using InterProScan software from the European Bioinformatics Institute (EBI). They are available on our Domain Download pages. Domain predictions for the four Aspergillus strains actively curated by AspGD are also available.

We now provide stable links to the current downloads of AspGD sequence files, GFF files and chromosomal features files. These links have the same names as the primary download files, except that the frequently-changing genome version identifier in the name is replaced with the constant term "current". Thus, when the names of the primary files change because of an update in the genome version, the names of the links will stay the same, facilitating automated access to the data.

We have also made general updates to the informative text on the download pages. We hope you will find these additions and improvements useful. (Posted January 24, 2013)

2012 AspGD News Archive

 

AspGD Infrastructure Improvements

We are pleased to announce that the AspGD servers are back online, now housed in a new data facility that provides a faster network and more stable environment than the previous location. All AspGD tools and resources are fully functional. We thank you for your patience and support during the outage. (Posted December 4, 2012)

Tool to Retrieve high-throughput data for genomic regions

We have added a new Retrieve Reads tool that allows you to retrieve high-throughput data, such as, RNA-seq reads for a specified genomic region or gene. Reads can be downloaded as a FASTA or FASTQ format file. (Posted November 1, 2012)

Historic Genome Assemblies in GBrowse

We have added new "Historic Tracks" to the AspGD Genome Browser for the A. nidulans, A. oryzae, and A. fumigatus genomes. These tracks provide an at-a-glance comparison of the current annotation version of these genomes to significant past versions. Use the "Select Tracks" tab in the browser to choose which historic assemblies to view. The order of individual tracks can be rearranged by "drag and drop," to customize the view as desired. (Posted September 21, 2012)

RNA-Seq data used to improve reference annotation for A. nidulans and A. oryzae

AspGD now includes RNA-Seq datasets for A. nidulans and A. oryzae, and these data have been used to make thousands of experimentally-supported refinements to the structural annotation of the genes in the A. nidulans and A. oryzae reference genomes in AspGD, using a PASA-based approach. The RNA-Seq data from the Caddick laboratory may be viewed and browsed in the A. nidulans Genome View browser, and the RNA-Seq data from the Wang laboratory and the Iwashita laboratory may be viewed and browsed in the A. oryzae Genome View browser. Genome View links are displayed on the Locus Summary pages for each gene, in the section labeled "RNA-Seq Data." All of the data may also be downloaded from AspGD. AspGD extends special thanks to Drs. K. Iwashita and Mark X. Caddick for sharing their unpublished RNA-Seq data. (Posted August 31, 2012)

Auto-suggest Feature in the AspGD Quick Search

We have added a new real-time suggestion feature to our Quick Search. As you type a query into the box, likely search terms from the database are now displayed in a pull-down menu below. We hope that this makes it easier for you to find the information you need, and we welcome your comments or suggestions. (Posted August 1, 2012)

AspGD Genome Browser Upgrade

We now feature a new and improved version of the Genome Browser in AspGD. For example, view a region of A. nidulans Chromosome VIII. In GBrowse2, the order of the data tracks in the display can be easily rearranged by drag-and-drop. In addition, the interface can smoothly switch among species, and between genomic and protein views, using the selections in the Data Source pull-down menu. The new interface provides tabs with track selection and various customization options. GBrowse is developed by the Generic Model Organism Database GMOD project. We look forward to your feedback. (Posted May 23, 2012)

New look for AspGD website

We are pleased to announce that AspGD has been upgraded to a more streamlined look, with a new home page and improved navigation options. It may be necessary to clear cached pages and restart your web browser for the new pages to render properly. AspGD thanks Yuri Amatnieks for the beautiful color images, now displayed on the AspGD home page. AspGD welcomes your feedback. (Posted May 14, 2012)

Intergenic Sequence Downloads

AspGD provides two new methods for obtaining intergenic sequences. (1) From the locus summary page of any feature (click here for an example), click on the pull-down menu under "Retrieve Sequences" on the right side of the page, select "DNA plus flanking intergenic seq for...", and then click "View". (2) From the sequence download page for an organism in AspGD (click here for an example); the relevant download files end with "_orf_plus_intergenic.fasta.gz", which contain protein-coding genes plus intergenic regions or "_other_features_plus_intergenic.fasta.gz", which contain other genes (for example, non-coding RNAs) plus intergenic regions. In all cases, we provide the sequence of the feature itself plus sequence extending upstream and downstream to the boundary of the next transcribed feature (exclusive). For protein-coding genes that boundary is the start or stop codon, for non-coding RNAs it is the 5' or 3' end of the mature RNA. (Posted April 24, 2012)

Improved Web Performance at AspGD

We are pleased to announce that the AspGD website has a new server. We are excited about the new speed and responsiveness of the AspGD web pages as a result of our migration to a new Linux system. Our benchmark testing indicates that the new system processes web pages and tools, such as BLAST, approximately 3 times faster than our old server. We thank you for your patience during the down-time on Tuesday March 20, 2012, which was necessary to switch the database over to the new server. We hope you will enjoy the improved performance of the AspGD website. (Posted March 22, 2012)

Updated Aspergillus fumigatus Af293 reference annotation

The sequence of the A. fumigatus Af293 nuclear genome has been updated to the version at CADRE, which differs from the previous AspGD version in the number of undetermined ("N") nucleotides used to represent gaps between contigs on chromosomes II and IV.

The structural annotation of each nuclear gene has been updated to the version contained in the CADRE set. New genes that are only present in the CADRE set have been added to AspGD. These genes have been assigned identifiers in the format Afu[chrom]g[number]. Genes that were present in the previous set at AspGD but which are not present in the CADRE set (i.e., genes deleted from the CADRE set) have now been deleted from the reference annotation, with the following exceptions, which have been retained:
  • Genes with an experimental description in AspGD
  • Genes with an ortholog or best hit in one or more of the other Aspergilli (excluding genes that have ONLY an ortholog or best hit annotated in the other A. fumigatus strain, A1163)
  • Genes with an ortholog or best hit in S. cerevisiae
  • Genes with annotated InterPro domain(s)
  • Genes with GO annotation in AspGD
  • tRNAs predicted by AspGD using tRNAscan-SE
All untranslated region (UTR) sequences annotated in the CADRE gene set are included in the new reference annotation set.

Mitochondrial genome sequence and annotation has been added. The sequence was generated by JCVI and the annotation was performed at the Broad Institute. Special thanks to Natalie Fedorova and Qiandong Zeng for the mitochondrial sequence and annotation, respectively. Mitochondrial gene identifiers have been assigned with the following format: AfuMt[number]. (Posted March 16, 2012)

New Aspergillus Strains Page at AspGD

We have added an "Aspergillus Strains" page to AspGD, with brief descriptions and references for some of the more commonly used laboratory strains, as well as lineage diagrams. If you would like to suggest additions, corrections, or updates to this list, please send a message to AspGD curators with details. (Posted February 10, 2012)

Large-scale Aspergillus fumigatus sequence data from JCVI available for viewing and download at AspGD

A. fumigatus isolates: 4 "reference" and 19 "target" Aspergillus fumigatus strains have been sequenced at the J. Craig Venter Institute (JCVI) using the Illumina platform. The list of sequenced strains includes (i) 7 drug resistant isolates, selected to facilitate the identification of new mechanisms of antifungal drug resistance (F series); and (ii) 12 genotypically linked isolates from 2 hospital outbreaks, included to validate the discriminatory power of existing genotyping markers (B series).

AspGD Locus summary pages (LSPs) for A. fumigatus genes contain a new Sequence Variation section (for example, see brlA), with links to short-read alignments displayed in the GenomeView browser, and to single nucleotide polymorphisms (SNPs) displayed in the GBrowse genome browser. The Sequence Variation section is located just below the Sequence Information section on each Locus Summary page.

To download the data, and for more information about the datasets themselves, please see our Large-Scale Datasets page. Files are available in VCF, BAM, and GFF format.

The SNPs displayed in GBrowse are defined relative to the Af293 reference sequence. We have added GBrowse tracks to display the SNPs observed in each sequenced strain individually, as well as a "SNP summary" track in which the color of the glyph indicates the relative frequency of the SNP; lighter blue color indicates that the SNP is observed in fewer strains and darker blue color indicates that the SNP is observed more frequently. The strains in which the SNP is observed are listed in the hover box displayed upon mouseover of a summary SNP glyph, along with the most common SNP nucleotide observed at this position. The polymorphism observed is displayed for each strain-specific SNP, and the associated quality score and read coverage is displayed in the hover box.

In the GenomeView browser, select the strains for which you would like to view short-read alignment data by clicking on the "eye" icon next to the strain name in the track list. You may browse by scrolling along the genome, zoom the view to see more or less detail, and navigate to specified positions in the genome or to individual genes (using the systematic gene name). General user documentation is available in the online GenomeView manual.

The A. fumigatus sequencing project at JCVI has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under contract numbers N01-AI30071 and / or HHSN272200900007C. The sequence data were supplied to AspGD by Natalie Fedorova, JCVI. The GenomeView browser was developed at the Broad Institute, and GBrowse is a GMOD project. (Posted January 12, 2012)

2011 AspGD News Archive

 

A. oryzae Data in AspGD

We are pleased to announce that we have now added A. oryzae information into AspGD. A. oryzae is the fourth Aspergillus species for which manually curated data are available in our database. The data loading is complete, and:
  • A. oryzae RIB40 sequence is now available in all of the AspGD tools
  • Each A. oryzae gene now has a Locus Summary page in the database
  • A. oryzae genome and annotation is available in the GBrowse Genome Browser
  • We have used tRNA-Scan to refine and update the A. oryzae tRNA predictions; like the protein-coding genes, the tRNA genes each have a Locus Summary page in the database
  • Genes have been assigned predicted function, process, and localization annotations (Gene Ontology terms) based on orthology to S. cerevisiae, A. nidulans, A. fumigatus, and A. niger
  • Additionally, protein-coding genes have been assigned predicted annotations based on protein motifs and domains (InterPro)
  • We have added new bibliographies and topic areas for A. oryzae to our Highlights in Aspergillus biology page.
  • Manual curation of the published scientific literature about A. oryzae genes is ongoing, and experimental data collected from the literature will continue to be added
We look forward to your feedback on the new A. oryzae species data in AspGD. (Posted November 21, 2011)

AspGD now contains comprehensive annotations for Aspergillus niger gene products

AspGD is pleased to announce that we have completed the manual curation of the gene-specific literature for A. niger and are further curating new literature as it becomes available. Because all of the available A. niger literature has been considered, we have now assigned Gene Ontology (GO) annotations to the root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" to gene products for which there are no experimental or computational data that would allow annotation with a non-unknown GO term. The evidence code for these "unknown" annotations, ND (No biological Data available), indicates that curators have searched for but have not found any relevant information as of the annotation date. AspGD is now "GO complete" for A. niger, meaning that each gene product has a GO annotation (including unknowns) in each of the three GO aspects. We look forward to your feedback on the new A. niger species data in AspGD. (Posted October 14, 2011)

A. niger Data in AspGD

We are pleased to announce that we have now added A. niger information into AspGD. The data loading is complete, and:
  • A. niger CBS 513.88 sequence is now available in all of the AspGD tools
  • Each A. niger gene now has a Locus Summary page in the database
  • A. niger genome and annotation is available in the GBrowse Genome Browser
  • We have used tRNA-Scan to refine and update the A. niger tRNA predictions; like the protein-coding genes, the tRNA genes each have a Locus Summary page in the database
  • Genes have been assigned predicted function, process, and localization annotations (Gene Ontology terms) based on orthology to S. cerevisiae, A. nidulans, and A. fumigatus
  • Additionally, protein-coding genes have been assigned predicted annotations based on protein motifs and domains (InterPro)
  • Manual curation of the published scientific literature about A. niger genes is ongoing, and experimental data collected from the literature will continue to be added
We look forward to your feedback on the new A. niger species data in AspGD. (Posted August 23, 2011)

Updated tRNA Annotation

We have updated the annotation of A. nidulans and A. fumigatus tRNA genes, based on predictions using tRNAscan-SE and comparisons with S. cerevisiae homologs. Changes include assignment of several A. nidulans proline tRNAs that were initially predicted to be pseudogenes. In addition, tRNA names and aliases have been updated, as outlined in the AspGD Nomenclature Guide. (Posted July 25, 2011)

New Additions to Highlights in Aspergillus Biology

AspGD curators have compiled a set of references on a variety of topics relevant to Aspergillus biology. We have recently added new bibliographies and topic areas for A. fumigatus. The reference lists are intended to provide a brief overview of each subject area, including many key reviews, and to serve as a resource for those new to research in Aspergillus biology. (Posted July 19, 2011)

Seeking Community Input

We have completed our curatorial review of the scientific literature about genes from A. nidulans and A. fumigatus, and would welcome you to review the information posted for the genes with which you are familiar. If there in any information that is inaccurate or incomplete, or if we are missing any references that should be cited, please let us know. We greatly appreciate your help in improving this community resource! (Posted July 18, 2011)

AspGD is on Facebook

AspGD now has its own page on Facebook, where we will post occasional updates and announcements.
To see the AspGD posts in your Facebook news feed, you may "like" the page. (Posted July 8, 2011)

Protein-domain-based Gene Ontology (GO) term predictions in AspGD

We have now added predictions about gene product function, role, and localization based on protein domains and motifs. Protein domains were determined using the InterProScan software from the European Bioinformatics Institute (EBI), and then domain-based Gene Ontology (GO) term assignments are made using the InterPro-to-GO mappings from GO Consortium web site. (Posted July 6, 2011)

Introducing Multispecies AspGD, with A. fumigatus curation

We are pleased to announce that we have now fully integrated A. fumigatus information into AspGD. We have curated the entire published experimental literature that describes A. fumigatus genes, and have made extensive updates to the AspGD database and software to store and query information across multiple species simultaneously.
    New and updated functionalities include:

  • Each A. fumigatus Af293 gene has its own Locus Summary page in AspGD; see, for example, the A. fumigatus veA/Afu1g12490 Locus Summary page.

  • The AspGD Locus Summary pages for each gene, in A. fumigatus as well as A. nidulans, contain a newly expanded section describing orthology within the Aspergilli, as well as orthologs in S. cerevisiae. Hyperlinks connect the AspGD Locus Summary pages between orthologous A. fumigatus and A. nidulans genes.

  • We have curated the entire published experimental literature that describes A. fumigatus genes, and have written gene descriptions, compiled citation lists, assigned Gene Ontology (GO) terms, and collected mutant phenotypes for every characterized gene. We have also leveraged orthology with A. nidulans and S. cerevisiae to make predictions about the function, role, and localization of A. fumigatus genes that have characterized orthologs in these other species. All of this information is fully available on the AspGD web site and in the AspGD downloadable files.

  • The sequence of the A. fumigatus Af293 genome is available in the AspGD searches.

  • We have added predicted tRNA genes for A. fumigatus.

  • We have implemented a multispecies BLAST tool, in which any subset of the multiple Aspergillus genomes can be selected and searched simultaneously.

  • The AspGD Search tools, including the Quick Search, BLAST, Gene/Sequence search, Ortholog Search, and the Pattern Matching Tool, have all been updated to query multiple species.

  • Quick Search results are now displayed in sections organized by species. Results that are not species-specific (e.g., individual GO terms, colleagues, references) are listed in a separate section on the results page.

  • The Protein Information page (Protein tab) has been updated and reorganized to consolidate the information and links from the Protein Info, Domains/Motifs and Physiochemical Properties subtabs onto a single, more browseable page.

  • Genome Snapshots are provided for both A. nidulans and for A. fumigatus, summarizing the status of the genome annotation on a daily basis.

We welcome your feedback on how we can improve the AspGD site and interface to make it more useful for your research. Please contact us any time. (Posted March 7, 2011)

2010 AspGD News Archive

 

Aspergillus nidulans transposable element genes now annotated in AspGD

Transposable element gene predictions were made at AspGD using TransposonPSI, an application based on PSI-BLAST similarity searches against a database of known transposons. You can use the AspGD Advanced Search tool to retrieve a list, by using the option to narrow your results to specific types of genes, and choosing the "transposable element gene" selection. (Posted October 15, 2010)

AspGD now contains comprehensive Gene Ontology annotations for Aspergillus nidulans nidulans gene products

AspGD curators have reviewed all of the gene-specific literature for Aspergillus nidulans nidulans and are curating the new literature on an ongoing basis. Because all of the available A. nidulans literature has been considered, we have now assigned Gene Ontology (GO) annotations to the root terms "molecular_function unknown", "biological_process unknown", or "cellular_component unknown" to gene products for which there are no experimental or computational data that would allow annotation with a non-unknown GO term. The evidence code for these "unknown" annotations, ND (No biological Data available), indicates that curators have searched for but have not found any relevant information as of the annotation date. AspGD is now "GO complete" for A. nidulans, meaning that each gene product has a GO annotation (including unknowns) in each of the three GO aspects. (Posted October 1, 2010)

Pattern Matching within Intergenic Regions

The AspGD Pattern Match tool now supports queries of the potential regulatory regions located between annotated features, in addition to the other chromosome- and feature-based sequence sets provided. To utilize this new feature, select "Intergenic regions" from the Sequence Database menu on the tool interface. You can search for specific sequence matches or for sequence patterns, using the character codes listed on the PatMatch tool page. (Posted September 1, 2010)

Links to gene knock-out cassettes at the FGSC

Each gene for which a knock-out cassette is available now has a "KO Cassette Available" link in the External Links section on its AspGD Locus Page (located just below the Sequence Information section). We have also added a link from the Phenotype Details page for each of these genes. The gene knock-out cassettes were produced at Dartmouth Medical School and have been shipped to the Fungal Genetics Stock Center (FGSC) as DNA suitable for transformation or amplification. More information about the resource is available on the FGSC web site, and a spreadsheet listing the cassettes and primers is available for download from the FGSC. (Posted August 20, 2010)

Highlights in Aspergillus Biology

A new bibliography resource is now available at AspGD. Curators have compiled a set of references on a variety of topics relevant to Aspergillus nidulans biology. The reference lists are intended to provide a brief overview of each subject area, including many key reviews, and to serve as a resource for those new to research in Aspergillus biology. (Posted July 20, 2010)

Sequences for Additional Aspergillus-related Species and Strains Now Available

AspGD now provides for download sequences from several Aspergillus and Aspergillus-related species and strains in addition to A. nidulans FGSC A4. The new additions include:
  • Aspergillus clavatus NRLL 1
  • Aspergillus flavus NRRL 3357
  • Aspergillus fumigatus A1163
  • Aspergillus fumigatus Af293
  • Aspergillus niger ATCC 1015
  • Aspergillus niger CBS 513.88
  • Aspergillus oryzae RIB40/ATCC 42149
  • Aspergillus terreus NIH2624
  • Neosartorya fischeri NRLL 181
All sequences are available on the Sequence Downloads Page. See the Sequence Help Page for additional information. We will add additional strains and species as their genomic sequences become available. (Posted July 9, 2010)

Announcing A. nidulans Annotation Version 5

We are pleased to announce the release of A. nidulans Annotation Version 5 in AspGD. This update merges the Version 4 annotation, which incorporates manually curated gene models from the Eurofung annotation, with a large set of updated gene model predictions from the Broad Institute. A more detailed description is found in the Version 5 release notes on the AspGD Sequence Documentation page. (Posted June 3, 2010)

New Community Resources

We have added two new resource pages to the AspGD web site, and we welcome your help in improving them. The Methods & Protocols page is a place for links to papers that serve as useful references for laboratory techniques. The Images and Movies page is a collection of still images and movies for Aspergillus researchers. Both may be accessed using the links under "Community Resources" on the menu on the left-hand side of the home page. Please contact us if you have images or citations that you would like to contribute. (Posted April 22, 2010)

Updated Gene Ontology terms and orthology mappings for Aspergillus nidulans genes

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 10503 GO annotations for 2470 A. nidulans genes in AspGD. (Posted April 6, 2010)

Multiple-species Aspergillus BLAST tool now available

AspGD now provides a BLAST tool to search multiple Aspergillus genomes at once. The genome sequences currently available are Aspergillus clavatus NRRL 1, Aspergillus flavus NRRL 3357, Aspergillus fumigatus A1163, Aspergillus fumigatus Af293, Aspergillus nidulans FGSC A4, Aspergillus niger ATCC 1015, Aspergillus niger CBS 513.88, Aspergillus oryzae RIB40/ATCC 42149, Aspergillus terreus NIH2624, and Neosartorya fischeri NRRL 181. We will add additional genomes as they become available. Try it out at the Multispecies Aspergillus BLAST page. (Posted March 19, 2010)

AspGD Protein Information Pages now available

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)

Aspergillus fumigatus Genome Browser now available in AspGD

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. The GBrowse software was written by Lincoln Stein as part of the Generic Model Organism Database (GMOD) Project. (Posted January 26, 2010)

2009 AspGD News Archive

 

Pseudogenes and Untranslated Regions in AspGD

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)

Updated Gene Ontology terms and orthology mappings for Aspergillus nidulans genes

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)

Aspergillus Genomic Online Community group

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)

AspGD paper in Nucleic Acids Research Database Issue

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)

Orthologs and syntenic regions

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.broadinstitute.org/. 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)

Aspergillus nidulans annotation update

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)

Predicted Gene Ontology terms and orthology mappings for Aspergillus fumigatus genes

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)

A. nidulans tRNA genes added to AspGD

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)

Announcing the Aspergillus Genome Database

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)


AspGD at the 25th Fungal Genetics Conference

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 contacted from our Suggestions and Questions page. 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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