I saw some plasmid genomes as big as bacterial genome and vice versa. I am wondering if there is any straight forward way to distinguish plasmid and bacterial genome. I know about the toxin and antibiotic resistant genes present in plasmids.
Plasmids are unlikely to have 'core' metabolic genes and wouldn't have any ribosomal proteins/RNAs. You could also look for tra genes, although they are not found on all plasmids.
If you're asking for a computational method to distinguish plasmids and, say, contigs of genomic DNA then have a look at cBar which uses pentamer patterns for classification.
Sorry Andreas this cBar is web site i think not existing any more and more over i tried to write to the author but i did not get any reply also. ........Crazzyyyyyyy...
Oh. I downloaded it before from http://csbl.bmb.uga.edu/~ffzhou/cBar/cBar.1.2.tar.gz which is now also broken. Looks like yet another piece of Bioinformatics software just died...
If you dont mind could you please send me one copy of that program, through email.
Unfortunately I don't have that copy anymore :(
This link is working.
Did anyone get cBar to work recently? I have downloaded it from the author's site http://csbl.bmb.uga.edu/~ffzhou/cBar/ and managed to compile it, but get no response when trying to execute it. I have bioperl and Weka installed, so that should not be a problem.
If not cBar, is there any other program out there that was designed to identify plasmid sequence?
Have you tried plasmidSPAdes?. It is other alternative.
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