I have managed to get a bacterial genome as a single contig. In looking at existing genomes, I notice that many of them have nucleotide #1 either as the beginning of the dnaA gene or a short distance upstream (perhaps at the actual origin?). On my genome I tried predicting the origin by GC skew and that said it was a bit downstream of dnaA. Right now these are at nucleotide 1.1 million something in my current assembly.
Should I bother to change this - is there some compelling rationale? Also, does anyone know tools that can do it, say on a Genbank file? I have been trying the EMBOSS tools but so far haven't found a good way to preserve the features.
Thanks in advance, Cliff