The symposium, which attracted close to 200 participants from both academic and commercial background in bioinformatics, focused on the state-of-the-art approaches to automatically annotate large genomes. The new journal Briefings in Bioinformatics will dedicate a whole issue at the end of this year to the advances in gene prediction that were revealed during this symposium.
The symposium featured thirteen speakers, all by invitation, and 24 specialist poster presentations.
The first day was dedicated to methodologies in gene prediction, and started of with Michael Zhang (Cold Spring Harbor Laboratory, USA) who described the application of discriminant analysis in DNA sequence motif recognition, especially with regard to splice sites and exons in the human genome.
Thomas Werner (GSF, Germany) continued with the identification of DNA sequence elements of transcription. This difficult task was achieved by modelling the organisation of promoters and using these versatile models to predict promoters in genomic sequence.
The usefulness of genome comparison was exemplified by Mikhail Gelfand (Centre for Biotechnology, Russia) who used it to predict regulatory patterns in complete bacterial genomes. He emphasised that currently there are no reliable algorithms [ed: for bacteria] that can match these predictions.
Anders Krogh (Center for Biological Sequence Analysis, Denmark) showed how combining ab-initio gene finding with database matches and other external information clearly improves performance, and even allows for errors and uncertainties.
Comparative analysis of human/mouse syntenic regions can be used to infer accurate gene predictions, Roderic Guigo (Municipal Institute of Medical Research, Spain) concluded in his talk. He also presented a new version of the GeneID program that is able to address longer genomic sequences than the current gene prediction programs.
Webb Miller (PSU, USA) presented on the same topic, and exemplified this with the program PipMaker, how valuable the mouse sequence is for the computational identification of human genes and other genomic regions.
The morning of the second day had as theme "Large-scale genome annotation projects". Suzanna Lewis (BDGP, USA) presented on the topic of managing those projects, exemplified by the "Annotation Jamboree", an experiment of co-operation between Celera, the Berkeley Drosophila Genome Project, and a team of experts to transform the process of annotation into a high-throughput operation.
Ewan Birney (EBI, UK) gave an overview of Ensembl, and explained how this system is used to automatically annotate the human genome, and how it keeps this annotation up to date.
The Genome Channel and Genome Catalog, developed and maintained by the Genome Annotation Consortium, were presented by Edward Uberbacher (ORNL, USA). Besides human sequence, these tools also represent all completed microbial genomes in a rich annotated view.
The afternoon session focused on the annotation of genomes, and began with a lecture by Klaus Mayer (MIPS, Germany) on Arabidopsis thaliana genome analysis as exemplified by chromosome 4 analysis.
Richard Durbin (Sanger Centre, UK) presented gene prediction in the C. elegans genome. Initially this was done via Genefinder, supplemented with other tools, but now a new system called GAZE is in development that uses flexible state specification for the definition of a gene and also takes prediction information from other sources into account.
The representation of gene function and process in genome databases was outlined by Michael Ashburner (EBI, UK). A Gene Ontology has been developed that will allow researchers to consistently annotate, and query for, these functions, processes, and cellular components in genomic databases.
Annotation and chromosome-wide analysis of the human chromosome 22 was presented by Tim Hubbard of the Sanger Centre. Lessons learned from chromosome 22 work indicate that automatic gene prediction is not reliable enough to predict genes, but a very valuable tool when combined with other information. At the Sanger Centre ab-initio gene finding is closely integrated with experimental work to annotate chromosome 22.
At the end of the symposium, plans were revealed by the organising committee to organise a larger conference on this topic next year, again on the Wellcome Trust Genome Campus, from 12 to 15 June.