Start codon analysis of Enterobacteriaceae

The sequences of established metabolic regulator genes from E. coli K-12 MG1665 were obtained from the Biocyc database and converted to a blast database for each regulatory gene with the command -makeblastdb. A homology search using nucleotide blast (blastn) was performed for each genome against every database, with parameters as follows: -max_target_seqs 100 -evalue 1e-5 -outfmt '6 qseqid qstart qend bitscore'. The best hit and 75 nucleotides on either end were cut out for each genome. Prodigal v 2.6.3 (Hyatt et al., 2010) trained on the E. coli K-12 MG1665 genome was then employed to identify potential start codons for each gene. Prodigal was run with standart parameters and the -s option to obtain the dailed scores for each potential start codon. This file was then used to get the relative start codon frequencies of all genes with the script "get_frequencies.txt". An example file to test the code is provided.