Author: Han Suh Kang; Katelyn McNair; Daniel A. Cuevas; Barbara A. Bailey; Anca M. Segall; Robert A. Edwards
Title: Prophage genomics reveals patterns in phage genome organization and replication Document date: 2017_3_7
ID: 0abutzb3_13
Snippet: Prophage coordinates from PhiSpy were used to extract nucleotide sequence data from the original bacterial genome. The nucleotide sequences are available as FASTA files from https://edwards.sdsu.edu/PhiSpy and https://figshare.com/articles/PhiSpy_prophage_predictions/3146656. Putative tRNA-encoding genes were identified from those genomes using tRNAscan-SE (22) . Modal codon usage was calculated from both the predicted prophage and the host genom.....
Document: Prophage coordinates from PhiSpy were used to extract nucleotide sequence data from the original bacterial genome. The nucleotide sequences are available as FASTA files from https://edwards.sdsu.edu/PhiSpy and https://figshare.com/articles/PhiSpy_prophage_predictions/3146656. Putative tRNA-encoding genes were identified from those genomes using tRNAscan-SE (22) . Modal codon usage was calculated from both the predicted prophage and the host genomes as described previously (23) , and tRNA use and modal codon use were compared using the χ 2 -test. The G+C content of the phage and host nucleotide sequences were calculated using custom-written Python scripts.
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