I'm looking at the gene sequences of a pair of enzymes and related processing proteins and am trying to figure out whether they are in the same operon, and where the operon begins and ends.
Hi ,
There are numerous tools available for operon prediction. You can try :
I would recommend you to use DOOR2 , but again the selection of tool entire depends on what analysis you want to perform.
Hope ,it helps.
Regards
Pankaj
Hi
You could also find some useful prediction tools in following links:
1- http://molquest.com/
2- http://rast.nmpdr.org/rast.cgi
3-http://www.genoscope.cns.fr/agc/microscope/home/index.php?
Best
Rahimi
Pankaj Kumar Singh I tried submitting the whole genome sequence and other required data to DOOR2 yesterday, but have not yet received a result. It said my request is pending, do you know how long it normally takes for a request to be processed? Though I'm guessing the whole genome sequence should take a while, is it possible I made a mistake in what I submitted?
Generally it takes 1-2 days max ...if you don't get your results...you can mail the tech support...
Actually there are many options as already mentioned, but here are some more:
https://operondb.jp/
http://biocomputo2.ibt.unam.mx/OperonPredictor/
https://rrndb.umms.med.umich.edu/
http://researchonline.lshtm.ac.uk/4648962/1/SLING-a-tool-to-search-for-linkedgenes-in-bacterial-datasets.pdf
Good fun!
Dear Mellisa
Use the following link. The link provide result in five minutes.
http://exon.gatech.edu/GeneMark/genemarks.cgi
Yesterday, 3 days after I messaged one of the people in charge of DOOR2, (6 days after I initially sent the sequence for analysis), I received the following message.
" The following message to was undeliverable. The reason for the problem: 5.4.7 - Delivery expired (message too old) '[Errno 61] Connection refused' "
I don't think the database is being upkept? I saw the website was copyrighted 2009-2013? I don't think it's being updated, and also may not be very reliable, because I saw information for a gene I was interested in being wrongly reported as "171bp" instead of "1719bp". I'm trying other options. Thanks though. Just though you should know that it seems like there's something wrong with that database. Pankaj Kumar Singh
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