US-AUSTRALIAN ACADEMIES JOINT WORKSHOP

US-AUSTRALIAN ACADEMIES JOINT WORKSHOP ON VERTEBRATE COMPARATIVE GENOMICS
Beckman Conference Centre, Irvine, California, 23-25 May 2007

Identification of highly diverged genes and application to mammalian comparative immunogenomics
by Tony Papenfuss

Dr Tony Papenfuss received his PhD in applied mathematics from Monash University, Melbourne Australia in 1999. After working as a mathematician in industry and a statistician on clinical cancer trials for several years, he became a post-doc in the Bioinformatics Division at the WEHI under Terry Speed. He is a member of the sequence analysis group and his interests include the evolution of immune and imprinted genes, and the development of new methods to identify and predict highly divergent homologues. He is also a member of the ARC Centre of Excellence in Kangaroo Genomics. At the WEHI, he also collaborates with biologists working on Plasmodium falciparum.

We recently completed the first survey of a marsupial immunome using the genome sequence of the South American opossum, Monodelphis domestica. The rationale for this work was to develop the opossum as a model for comparative immunology, to study the evolution of mammalian immune genes and less directly, to gain experience and develop tools for use on Australian marsupials.

We found several important families of immune genes were highly diverged in the opossum and were difficult to detect using straightforward homology searches. Consequently, we developed several approaches that made use of profile HMM searches of the genome, followed up by gene prediction. We are now applying these approaches to the platypus genome.

In this talk I will discuss the approaches used and some interesting results in MHC class I genes, antimicrobials and platypus venom genes.

Contact details:
Bioinformatics Division
The Walter and Eliza Hall Institute of Medical Research
1G Royal Pde, Parkville VIC 3050.

Tel: (+61) 3 9345 2627
Fax: (+61) 3 9347 0852
E-mail: papenfuss@wehi.edu.au
Web: http://bioinf.wehi.edu.au/contacts/details_papenfuss.html