New and Noteworthy

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)

• A. nidulans Genome Snapshot
• A. fumigatus Genome Snapshot
• A. niger Genome Snapshot
• A. oryzae Genome Snapshot
• New papers added to AspGD this week.
• View Genome-wide Analysis papers in 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)

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)

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)

Click here to view archived news items.