getting and formatting dnaA gene data

[colindaven]

For those coming to this tool in 2026, there are several things you should know which may not be obvious. Using dnaA data is critical to getting the tool fixstart to work well.

The download of dnaA did not work for me, whether behind a proxy or not

Fix - this unmerged code may help those (at least those who are not using pre built containers) to get the download working
https://github.com/sanger-pathogens/circlator/pull/182/changes

You can get a dnaA fasta (this must be in nucleotide not amino acid format!) from this repo here - but it is old

wget https://raw.githubusercontent.com/sanger-pathogens/circlator/refs/heads/master/circlator/data/dnaA.fasta

It seems you can get protein sequences easily from Uniprot manually but then need to reverse translate them into DNA

Did it work ?

# the detailed.log from fixstart step looks like this if successful

Using the following promer matches to circularize contigs:
1       1368    1       1368    1368    1368    82.28   704514  1368    1  xxxx yyyyy