This is a conference report written by the beneficiaries of our travel fund.
Click here to read more about the fund and apply yourself
I would like to thank the BSPP for providing a Travel Grant that enabled me to attend the TIGR Genome Annotation Workshop. As part of the rice genome sequencing and annotation project TIGR hold this workshop annually to provide training in bioinformatics, enabling scientists to exploit this rice resource and the processes involved in structural and functional genome annotation in general. The 2006 workshop, held at TIGR in Maryland, USA, ran from the 26th-30thJune and involved 30 scientists from around the world, including Australia, Africa, South America and Japan as well as the USA and UK.
The group represented many different areas of research in plant science and levels of expertise in bioinformatics, yet the form and content of the workshop allowed each individual to address their own personal objectives whilst simultaneously providing an overall impression of the annotation process, from sequencing to functional annotation. The subjects covered were of benefit both to those intending to set up annotation pipelines and researchers and students wishing to exploit the rice resource or its annotation methods for their own projects.
The workshop began with lectures given by members of the annotation team focusing on how high quality sequence data is assembled, providing an accurate basis for annotation. The highly automated annotation pathway then begins with the prediction of non overlapping coding segments by evaluating features of the DNA sequence such as start and stop codons, promoters, introns and exons. Full Length cDNA and EST evidence is invaluable in the accurate resolution of gene structure, and the automatedPASA (Program to Assemble Spliced Alignments) pipeline allows transcript alignments to be incorporated into gene structure annotations, providing evidence for alternative splicing and UTRs. If an annotation update passes stringent validation tests when compared to the existing gene model, models can be merged, split or updated on the basis of this transcript evidence.
Whilst learning about this process computer exercises demonstrating various alignment tools and the algorithms behind them were completed. Further lectures and exercises covered functional annotation and expression data resources such as Massively Parallel Signature Sequencing (MPSS), as well as an introduction to the genome resources being developed for maize. The workshop culminated in the group attempting to annotate a locus of the rice genome.
As a 1st yr PhD student with little previous bioinformatics experience this workshop provided the opportunity to develop my understanding of how publicly available sequence data is produced. My PhD project involves investigating the translation of disease resistance signalling pathways between Arabidopsis and the cereals and in explaining how gene models are predicted the workshop has allowed me to more confidently select and investigate candidate orthologues, before experimentally characterising those genes. Attending this workshop at TIGR will greatly enhance the bioinformatic analyses involved in my PhD project and I am extremely grateful to the BSPP for their support.
Ellen Colebrook, John Innes Centre
