Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the Mycobacterium Neighborhood

Pope, Welkin H.; Jacobs-Sera, Deborah; Russell, Daniel A.; Rubin, Daniel H. F.; Kajee, Afsana; Msibi, Zama N. P.; Larsen, Michelle H.; Jacobs, William R.; Lawrence, Jeffrey G.; Hendrix, Roger W.; Hatfull, Graham F.

To measure codon selection, a second codon usage table (f o ) was tabulated, limited to genes experiencing strong codon selection. For bacterial genomes, this table was constructed from homologues of Sharp's set of 40 genes whose products participate in translation (36) . For Patience, this table was constructed in three steps. First, a codon usage table was generated from 20% of the genome using the genes with the most extreme value of codon usage bias as determined by 2 (where expected codon usage is calculated from the nucleotide composition). Next, adaptive codon enrichment (ACE u ) values (25) are calculated for all genes as described previously (25) , using this table to represent codon frequencies under codon selection (f o ) and the frequencies of codons among all genes in the Patience genome to represent codon frequencies expected from mutational processes alone (f N (34) , and Phamerator (35) .