Author: 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.
Title: Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the Mycobacterium Neighborhood Document date: 2014_12_2
ID: 7m53i1h9_24
Snippet: DNA sequencing. Patience was isolated using standard methods as described previously (7, 30) , and the genome was sequenced using 454 technology at the University of Pittsburgh's Genomics and Proteomics Core Laboratories; a total of~45,000 reads were assembled to yield an average (34) , and Phamerator (35) . The Phamerator database used for genomic comparisons was Mycobacteriophage_285. Phams were built using BLASTP and/or ClustalW, with similari.....
Document: DNA sequencing. Patience was isolated using standard methods as described previously (7, 30) , and the genome was sequenced using 454 technology at the University of Pittsburgh's Genomics and Proteomics Core Laboratories; a total of~45,000 reads were assembled to yield an average (34) , and Phamerator (35) . The Phamerator database used for genomic comparisons was Mycobacteriophage_285. Phams were built using BLASTP and/or ClustalW, with similarity cutoff E values of 10 Ϫ50 and 32.5% similarity or better as described elsewhere (35) . Codon usage and codon selection. Codon usage resulting from mutational biases was estimated using the collection of all genes from a genome. The fraction (f) of each codon for a given amino acid was calculated as the ratio of the codon count to the amino acid count. Relative synonymous codon usage (RSCU) normalizes codon frequencies so that the sum of RSCU for codons of each amino acid is equal to the number of synonymous codons for that amino acid.
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