<p>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 &quot;1&quot; of the finished sequence is (or you could also say with which gene the sequence starts).</p>

<p>I heard some rules already like putting the OriC at the beginning.</p>

<p>Does anyone have a good paper/source for that?</p>

<p>Thanks!</p>

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.