We now have in hand the nearly complete DNA sequence for the human genome and for several other genomes. We also have relatively complete predictions as to what sub-regions in those sequences are genes. A major task now is to understand the function of those genes and the other parts of the genome, such as gene regulatory sequences. This is the goal of "functional genomics".

To facilitate this analysis, online annotation databases are being developed and continually updated so that they contain comprehensive summaries of the functional information known from previous biological experiments. New experimental results and information - either biological or computational - can then be readily analyzed in relation to, and integrated with, the information in these databases.

For example, newly discovered mutations (single nucleotide polymorphisms, or "SNPs") in human DNA sequences can be assessed for potentially pathogenic function by comparison to previously characterized disease-causing mutations annotated in human disease and mutation databases such as OMIM and HGMD. As another example, potential gene regulatory regions identified by computational analysis of the Drosophila or C. elegans genomes can be assessed for potential function by comparing their positions in the genome with those of known or predicted genes in annotation databases such as Flybase and Wormbase.

Specific examples of functional genomics will be presented from a biologist's perspective, including the molecular and genetic logic used in designing the experiments and in interpreting the results. Recently developed BioPerl-related modules and programs such as Bio::DB::GFF and Bio::Graphics, and the Generic Genome Browser, will be used to demonstrate the ready integration of new experimental data with existing annotation databases.