Hi,
I want to predict operons on entire bacterial genomes (already annotated). I used to use operon-mapper ( https://academic.oup.com/bioinformatics/article/34/23/4118/5040321), which is great but it has been "under maintenance" for weeks now and I really need one now.
MicrobesOnline doesn't support private genome hosting anymore and I think that the DOOR website is now down.
If you know any other tool, online or not, that would allow the genome-wide prediction of operons in complete, annotated bacterial genomes, that would be of great help to me.
Thanks
Julian
Dear Julian,
There are many tools are found on NCBI or GenBank website to predict the operon of bacteria genome.
Kind regards
Hi,
NCBI site is very past for this work and it content several tools .
Hi Julian,
You may want to check these websites:
http://exon.gatech.edu/GeneMark/genemarks.cgi
https://operondb.jp/
Hi Julian,
Please refer this article
https://academic.oup.com/bioinformatics/article/34/23/4118/5040321
Thanks
Hi all, I am still looking for a tool to predict operon on entire, annotated bacterial genomes. Any suggestion is welcome.
To respond to the previous answers:
Roshan Kumar, as I say in my question, operon-mapper (the paper you link) is not working anymore.
Sayanta Bera, thank you for your suggestions, I tried GeneMarks but it only creates new annotations for genomes with gene position and doesn't say which genes are in operons together, which is what I want. Concerning Operondb, I see that there are many genomes with predicted operons, but I haven't found a tool to predict operons on genomes that are not on the database, is there one on the website ? Because my genomes are not on there, so I'm looking for a tool where I can upload my genomes.
Sunagar Raju, could you precise which tool from the website you linked can do operon prediction as I haven't found it ?
Khwam R Hussein & Alaa Kareem Niamah , could you precise which NCBI tool can do operon prediction as I haven't found it ?
There are several of such tools. Please follow the link suggested by Roshan Kumar to Operon-mapper and PROCSIMO in the document suggested below. Conference Paper Operon Prediction in Bacterial Genomes
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