Analysis and prediction of gene splice sites in four Aspergillus genomes

Research output: Contribution to journalJournal articleResearchpeer-review

Several Aspergillus fungal genomic sequences have been published, with many more in progress. Obviously, it is essential to have high-quality, consistently annotated sets of proteins from each of the genomes, in order to make meaningful comparisons. We have developed a dedicated, publicly available, splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at
Original languageEnglish
JournalFungal Genetics and Biology
Volume46 Suppl 1
Pages (from-to)S14-8
Publication statusPublished - 2008
Externally publishedYes

Bibliographical note

Keywords: Aspergillus; Computational Biology; Genome, Fungal; RNA Splice Sites; Software

ID: 18947070