Summary

• The current challenge in bioinformatics of bacteriophage genomes is to overcome the large percentage of genes with no information concerning their function found in many new phage genomes.  Approaches that show promise include:
• Sequence lots of novel phages to allow proteins to form families.
• Use HMM methods to extend families to maximum extent.
• Make use of focused libraries to improve signal to noise in seeking homologues.
• Automate methods to run across all genes in each new (or old) virus and automatically collate results.
• Seek improved visualization methods to emphasize patterns found in comparative analysis across multiple genes and viruses.
• Seek individual gene trees that can be assigned a time scale for use in quantitating rates of rearrangment of various segments of the genome.
• Create improved models for distinguishing coiled coil structures.
• Seek opportunities where proteomics experiments might assign functions to multiple genes at once.