Distinguishing Bacterial And Plasmid Genomes

Question

[Pappu]

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.

Answer 1

[cts]

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.

Answer 2

[Andreas]

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.

Andreas

[HG]

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...

[Andreas]

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...

[HG]

If you dont mind could you please send me one copy of that program, through email.

[Andreas]

Unfortunately I don't have that copy anymore :(

[Pappu]

This link is working.

[bols]

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?

Answer 3

[jilguero888]

Have you tried plasmidSPAdes?. It is other alternative.