Question: Distinguishing Bacterial And Plasmid Genomes
0
gravatar for Pappu
5.4 years ago by
Pappu1.9k
Pappu1.9k wrote:

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.

genome • 3.2k views
ADD COMMENTlink modified 20 months ago by jilguero88810 • written 5.4 years ago by Pappu1.9k
2
gravatar for cts
5.4 years ago by
cts1.6k
Pasadena
cts1.6k wrote:

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.

ADD COMMENTlink written 5.4 years ago by cts1.6k
1
gravatar for Andreas
5.4 years ago by
Andreas2.4k
Singapore
Andreas2.4k wrote:

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

ADD COMMENTlink written 5.4 years ago by Andreas2.4k

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...

ADD REPLYlink written 5.2 years ago by HG1.1k

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...

ADD REPLYlink written 5.1 years ago by Andreas2.4k

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

ADD REPLYlink written 5.1 years ago by HG1.1k

Unfortunately I don't have that copy anymore :(

ADD REPLYlink written 5.1 years ago by Andreas2.4k

This link is working.

ADD REPLYlink written 5.1 years ago by Pappu1.9k

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?

ADD REPLYlink written 3.5 years ago by bols0
0
gravatar for jilguero888
20 months ago by
jilguero88810
United States
jilguero88810 wrote:

Have you tried plasmidSPAdes?. It is other alternative.

ADD COMMENTlink written 20 months ago by jilguero88810
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