Providing researchers access to essential genome annotation tools

Community consultations are an opportunity for researchers to describe their challenges and research infrastructure needs. BioCommons has worked with a growing number of researcher communities who self-nominate around particular informatics methods. In response to requests from the Genome Annotation community for automatic genome annotation pipelines, BioCommons has made Fgenesh++ available for use by Australian-based research groups and research consortia.

Fgenesh++ is a bioinformatics pipeline for automatic prediction of genes in eukaryotic genomes. It can produce fully automated genome annotations of a quality similar to manual annotation, and is extremely fast compared to some other automated genome annotation pipelines.

It works by: (a) performing ab initio gene prediction; (b) running predicted amino acid sequences of all potential exons through a non redundant protein sequence database; and (c) running a second round of gene prediction with higher scores assigned to exons homologous to known proteins. 

To overcome the hurdles that many researchers face when wanting to try out licensed software, BioCommons entered into an agreement with Softberry that allows for a limited number of users to share access to Fgenesh++. Access is through a booking system which is managed by the Pawsey Supercomputing Research Centre.

BioCommons’ Community Engagement Officer, Dr Tiff Nelson, oversaw the provisioning of Fgenesh++ and has been impressed to see its rapid uptake:

It is great to have already facilitated the annotation of novel animal and plant genomes for the benefit of both conservation and agricultural research outcomes.

One group that has already benefitted from the service is the Australasian Wildlife Genomics Group, School of Life and Environmental Sciences at the University of Sydney, where Postdoctoral Bioinformatician, Dr Kate Farquharson, said:

The Fgenesh++ service has helped us easily and efficiently annotate multiple diverse genomes to a high standard.

Fgenesh++ is installed on computational resources provided by the Pawsey Supercomputing Research Centre and supported by Bioplatforms Australia, which is enabled by NCRIS. 

Learn more about how you can apply to access BioCommons’ Australian Fgenesh++ Service.

Our Genome Annotation Infrastructure Roadmap for Australia presents a national vision for shared national infrastructure that will help researchers undertake genome annotation. It was developed through our engagement with a broad range of Australian researchers working across a wide variety of taxa. If you would like to join in the conversation, let us know what else is required and also receive updates on new services coming online, please sign up to our google group.