Author: Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C
Title: A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences Document date: 2018_8_7
ID: yiqdsf9z_9
Snippet: To explore the possibility of using this method to screen for candidate overlapping ORFs, we calculated both the sensitivity and false discovery rate of the codon permutation test, the synonymous mutation test, and a combined test that requires an ORF to be larger than expected by both the codon permutation and synonymous mutation test. As there are too few coding regions within a single genome to estimate the sensitivity and false discovery rate.....
Document: To explore the possibility of using this method to screen for candidate overlapping ORFs, we calculated both the sensitivity and false discovery rate of the codon permutation test, the synonymous mutation test, and a combined test that requires an ORF to be larger than expected by both the codon permutation and synonymous mutation test. As there are too few coding regions within a single genome to estimate the sensitivity and false discovery rate with sufficient precision, we estimated the population sensitivity and false positive rate across a subset of viruses (linear RNA viruses) known to contain many overlapping genes (see Materials and Methods section). Accordingly, whole genome sequences were downloaded from 2548 reference linear RNA viruses available on GenBank; this produced a total of 6408 coding regions that were used to estimate the sensitivity and false discovery rate of each test.
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