High-throughput sequencing and functional genomics technologies have given us the human genome sequence as well as those of other experimentally, medically and agriculturally important species, and have enabled large-scale genotyping and gene expression profiling of human populations. Databases containing large numbers of sequences, polymorphisms, structures and gene expression profiles of normal and diseased tissues are rapidly being generated for human and model organisms. Bioinformatics is thus rapidly growing in importance in the annotation of genomic sequences, in the understanding of the interplay among and between genes and proteins, in the analysis the genetic variability of species, in the identification of pharmacological targets and in the inference of evolutionary origins, mechanisms and relationships. This proceedings contains an up-to-date exchange of knowledge, ideas, and solutions to conceptual and practical issues of bioinformatics, by researchers, professionals, and industrial practitioners at the 5th Asia-Pacific Bioinformatics Conference held in Hong Kong in January 2007.