I want to find operon predictions for bacterial genomes. I have got partial genomes with prediction via using microbeonline server, operondb and door2 . Door2 server is currently inaccessible since two months. I want to know if there is any program or script that I could use such that I can find operon predictions in bacterial genomes without having to input one by one in a GUI based server. Please suggest a command line program or any way I can automate this problem.
You might be able to find the code in here:ftp://vimssftp.lbl.gov/pub/UnsupervisedOperons/Genomics/seq/ but It's a mess. Honestly, I think that poly-cistronic units (operons are something else, See Jacob and Monod early papers) differ between bacteria. After watching a huge variability in RNAseq data I can say that even in the well annotated E. coli there are a lot of alternative transcripts. The operon predictor everyone uses (Arkin lab) is trained on old data, pre-Illumina, this should also be taken into account.
There are lots of tools available for operon prediction, but the ones I know about are not very current. For genomes sequenced before 2011, you can download full predictions here. Try here if you want to upload your own sequence. Also, lots of tools are listed on the right-hand side of this page.