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_10
Snippet: The codon permutation, synonymous mutation and combined test all rely on detecting overlapping ORFs that are larger than expected by random chance. Consequently, the sensitivity of these tests will depend on how much of a gene is overlapping (denoted as overlap length). The sensitivity and false discovery rate will also be dependent on the P value cutoffs used to determine if an ORF is larger than expected by random chance, with higher P values p.....
Document: The codon permutation, synonymous mutation and combined test all rely on detecting overlapping ORFs that are larger than expected by random chance. Consequently, the sensitivity of these tests will depend on how much of a gene is overlapping (denoted as overlap length). The sensitivity and false discovery rate will also be dependent on the P value cutoffs used to determine if an ORF is larger than expected by random chance, with higher P values providing higher sensitivity at a cost of greater false discovery. To understand these dependencies, receiver operator characteristic (ROC) curves were generated across a range of P values, and across a range of overlapping gene lengths for all three tests ( fig. 3 ). The number of true overlapping ORF's used in this sensitivity set ranged from 958 for overlapping ORF lengths greater than 0 nucleotides, to 199 for overlapping ORF lengths greater than 300 nucleotides.
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