The Origin Of Replication And Positive And Negative Strand In Genbank File

Question

[Pappu]

I am trying to analyze the loci of a gene in various bacterial genomes. Sometimes the gene appears at the beginning/end of the genome in the embl/genbank file. I am wondering if the starting base of the genome has any connection with the origin of replication (ORi). Also if the selection of positive and negative strand are random. If yes, I will put my gene of interest in positive strand in all genomes for easier comparison.

Answer 1

[Emily]

The start is just the origin of sequencing, which is not necessarily the origin of replication. You can see quite nicely in Ensembl Bacteria, which uses EMBL-Bank genome and annotation files directly, without processing to find the origin of replication.

Here's a genome where the origin of sequencing is the origin of replication. The origin of sequencing is shown at the top, as a red arrow. The obvious GC and gene skew on either side of ther chromosome clearly show demonstrate the positions of the origin and terminus of replication.

Here's a genome where it's not. The origin of sequencing is, again, at the top. But the GC skew seems to be ~60º away from vertical, suggesting that the origin and terminus are at the 4 o'clock and 10 o'clock position (no idea which is which).

Here's a genome where there's no way of knowing. No GC or gene skew, so the origin of replication could be anywhere.