- The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. [PMID: 24194595]
Gustavo C Cerqueira, Martha B Arnaud, Diane O Inglis, Marek S Skrzypek, Gail Binkley, Matt Simison, Stuart R Miyasato, Jonathan Binkley, Joshua Orvis, Prachi Shah, Farrell Wymore, Gavin Sherlock, Jennifer R Wortman
Nucleic acids research 2014:42(Database issue)
53 Citations (Google Scholar as of 2016-01-30)
Abstract: The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community. In addition to being a repository and central point of access to genome, transcriptome and polymorphism data, AspGD hosts a comprehensive comparative genomics toolbox that facilitates the exploration of precomputed orthologs among the 20 currently available Aspergillus genomes. AspGD curators perform gene product annotation based on review of the literature for four key Aspergillus species: Aspergillus nidulans, Aspergillus oryzae, Aspergillus fumigatus and Aspergillus niger. 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. 2012). In this update, we report substantive structural annotation improvements for A. nidulans, A. oryzae and A. fumigatus genomes based on recently available RNA-Seq data. Over 26 000 loci were updated across these species; although those primarily comprise the addition and extension of untranslated regions (UTRs), the new analysis also enabled over 1000 modifications affecting the coding sequence of genes in each target genome.
- The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. [PMID: 22080559]
Martha B Arnaud, Gustavo C Cerqueira, Diane O Inglis, Marek S Skrzypek, Jonathan Binkley, Marcus C Chibucos, Jonathan Crabtree, Clinton Howarth, Joshua Orvis, Prachi Shah, Farrell Wymore, Gail Binkley, Stuart R Miyasato, Matt Simison, Gavin Sherlock, Jennifer R Wortman
Nucleic acids research 2012:40(Database issue)
64 Citations (Google Scholar as of 2016-01-30)
Abstract: The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD curators have now completed comprehensive review of the entire published literature about Aspergillus nidulans and Aspergillus fumigatus, and this annotation is provided with streamlined, ortholog-based navigation of the multispecies information. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. AspGD also provides resources to foster interaction and dissemination of community information and resources. We welcome and encourage feedback at email@example.com.