Question: Position 1 in closed circular genome.
0
gravatar for Cliff Beall
2.2 years ago by
Cliff Beall450
Ohio
Cliff Beall450 wrote:

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

bacteria genome • 657 views
ADD COMMENTlink modified 2.2 years ago by natasha.sernova2.9k • written 2.2 years ago by Cliff Beall450
1

Where to put start for assembled genome/plasmid

ADD REPLYlink written 2.2 years ago by piet1.4k

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.

ADD REPLYlink written 2.2 years ago by Cliff Beall450
1
gravatar for natasha.sernova
2.2 years ago by
natasha.sernova2.9k
natasha.sernova2.9k wrote:

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!

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by natasha.sernova2.9k

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.

ADD REPLYlink written 2.2 years ago by Cliff Beall450
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