Some exciting new tool updates; a couple of tools to help you filter GFF3 files in your analyses based on Shine Dalgarno sequences and “Phage Start Codons”, and an update to the CPT’s own Codon Optimizer
Sometimes in your analyses you find yourself producing a gff3 file of naive gene calls, and have thousands of “possible” genes to dig through on your way to reliable and useful results. Two steps you can easily atabdd to your workflows now include filters to ensure that those called features have upstream SD sequences, and have a start codon that’s appropriate for phages as table 11 is sometimes too broad (7 start codons! ATA, ATT, ATC, ATG, TTG, CTG, GTG; most phages only use ATG, GTG, and TTG)
Additionally we made an update to the Codon Optimiser (TAMU, Public) tool so now it can automatically avoid specific sequences, whether they’re from a built-in list of Enzymes cut sites or manually specified sequences. The tool will automatically try tens of thousands of possible alternatives if it detects a sequence you have blacklisted.