SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Getting the part of a genome that was NOT covered by a samples reads naymikm Bioinformatics 4 10-28-2014 08:36 PM
2-part TCGC: The Clinical Genome Conference | June 25-28 | Boston, MA Pavolga Events / Conferences 2 05-14-2013 09:26 AM
RNA-seq(tophat|cufflinks) on part of a genome: special considerations? brachysclereid Bioinformatics 2 02-27-2011 10:31 PM

Reply
 
Thread Tools
Old 06-11-2014, 02:30 AM   #1
Mona
Member
 
Location: Uppsala

Join Date: Feb 2010
Posts: 27
Default Plasmids part of core genome

Hi,

I am trying to compare the core genome of 7 different species bacteria. One of them also contains plasmid sequences. Should I keep the plasmid sequence also in the analysis or not?

Last edited by Mona; 06-11-2014 at 02:35 AM.
Mona is offline   Reply With Quote
Old 06-11-2014, 07:29 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

One way of looking at this is that 6 of your 7 species do not have plasmid information so how could you do the comparison even if you wanted to do so? In general I would consider the term "core genome" to not include non-chromosomal elements such as plasmids.
westerman is offline   Reply With Quote
Old 06-16-2014, 05:32 AM   #3
Mona
Member
 
Location: Uppsala

Join Date: Feb 2010
Posts: 27
Default

Quote:
Originally Posted by westerman View Post
One way of looking at this is that 6 of your 7 species do not have plasmid information so how could you do the comparison even if you wanted to do so? In general I would consider the term "core genome" to not include non-chromosomal elements such as plasmids.
Thanks westerman,
Thats quite logical But isn't it possible that plasmids having chromosal genes?
Mona is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:38 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO