If you have a closed bacterial genome or plasmid, what are the general rules where to put the start. With start I mean where the base "1" of the finished sequence is (or you could also say with which gene the sequence starts).
I heard some rules already like putting the OriC at the beginning.
Does anyone have a good paper/source for that?
Thanks!
There is no general rule, but please avoid to linearize your circular sequence within a coding sequence. There are many plasmids in Genbank where interesting genes like antibiotic resistance determinates have been cut into two halves. Its always a pain to work with such sequences.
In most Eubacterial chromosomes the origin of replication is located between the highly conserved genes rpmH and dnaA. For Firmicutes it is a good choice to place the start codon of dnaA on position 500. In some species there may exist isolates where the orientation of the oriC region is reversed with respect to the majority of the chromosome. With such an isolate it may be appropriate to make rpmH the first gene on the linearized chromosome and dnaA the last.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
OK, that helps me already a lot
Follow up question: How do you detect the exact position of origin of replication in plasmids and in genomes? I guess they are pretty much the same in general, right?
At the moment I want to do it specifically for Lactobacillus.
The chromosomal origin of replication is located between rpmH and dnaA, I would guess that Lactobacillus is not different from other Firmicutes.
With plasmids there is not such a simple rule.There exist different mechanismens of replication, especially small plasmids (sometimes called cryptic plasmids) are using rolling circle. Maybe you can blast putative rep genes and try to find an ortholog on a well annotated sequence.