1. The reader who decides to address these problems is expected to use the tools described in this chapter including general-purpose ones such as different versions of BLAST. In most cases, it is...

1. The reader who decides to address these problems is expected to use the tools described in this chapter including general-purpose ones such as different versions of BLAST. In most cases, it is advisable to apply more than one method when trying to solve a problem. The reader should keep in mind that some of the problems may not have a single ‘‘correct’’ solution but rather one or perhaps even two or three most likely solutions.

2. Three archaeal species, M. jannaschii, M. thermoautotrophicum, and A. fulgidus, typically are found in COGs together. The fourth species, P. horikoshii, is frequently missing from these COGs (see the table of co-occurrence of genomes in COGs, which is available on the COG Web site). How do you explain this? What kind of genes are absent from P. horikoshii?