A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences

Schlub, Timothy E; Buchmann, Jan P; Holmes, Edward C

A search for sequences homologous to the 29 newly discovered overlapping ORFs was performed by aligning their protein sequences to the NCBI nt database using tblastn (TBLASTN 2.6.0þ). The e-value threshold was set to 0.001 while all other settings were set to their default values. The results were stored in a SQLite3 database (3.24.0). For homologous sequence detection the alignments were filtered to include only alignments with similarity !90% and length !90% of the corresponding ORF sequence. From each filtered alignment, the NCBI accession for the query (ORF) and subject were extracted and the corresponding taxid and lineage obtained using NCBI Entrez. A python tool taxmax.py was developed (https://gitlab.com/janpb/taxmax.git) to compare the NCBI lineage from each ORF and its aligned sequence. The similarity between two lineages is described as a score between 0 and 1. A score of 0 indicates no similarity between lineages while a score of 1 indicates both sequences have the same NCBI lineage. For each alignment The alignments positions were compared to check for orthologous positions.