Dear BioStars
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
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Cliff Beall
Dear Cliff,
It turned out, many years ago I wrote a paper about identification of bacterial origin.
http://bib.oxfordjournals.org/content/9/5/376.full
I hope it will help you. You will find all the existing at that time tools to determine where the origin is, etc.
Very few things have changed since that time.
Yes, that's true, the origin approximate position is chosen somewhere
around the middle position of the spacer sequence between a start of DnaA-gene and the end of a previous gene.
Good luck!
Thanks, that is useful. Based on that I will treat the GC skew estimate as approximate and go with dnaA. I do see three repeats that might bind DnaA in the region between the gene and rpmH as well.
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Where to put start for assembled genome/plasmid
Thanks, I hadn't found that question. It prompted me to look for the rpmH gene by tblastn, which turned out had been missed just upstream of dnaA.