SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to identify the secretion system in a newly sequenced bacterial genome? ontheway Bioinformatics 4 09-25-2013 03:48 PM
Bacterial contamination in salival sample ulz_peter Sample Prep / Library Generation 2 02-20-2012 11:57 AM
mRNA from Bacterial sample for trueseq Garyron Sample Prep / Library Generation 9 08-16-2011 01:42 AM
Bacterial genomic DNA sample mazinga Sample Prep / Library Generation 9 01-31-2011 10:47 AM

Reply
 
Thread Tools
Old 07-02-2013, 12:33 PM   #1
shiningway
Junior Member
 
Location: US

Join Date: Mar 2009
Posts: 7
Default How to identify different bacterial strains in the same sample

I have Illumina sequencing of a bacterial sample collected from a patient. I suspect it's a mixture of multiple strains of the same bacteria, but I don't which strains are in there. Is there anyway to identify

1. if this sequence sample is a mixture of different strains?

2. how many and what strain are in there?

Thanks.
shiningway is offline   Reply With Quote
Old 07-02-2013, 12:37 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,138
Default

How to do this in practice: http://seqanswers.com/forums/showthread.php?t=16812

Analysis (see post #2) in this thread: http://seqanswers.com/forums/showthread.php?t=31565

Last edited by GenoMax; 07-02-2013 at 12:43 PM.
GenoMax is offline   Reply With Quote
Old 07-02-2013, 01:11 PM   #3
shiningway
Junior Member
 
Location: US

Join Date: Mar 2009
Posts: 7
Default

Thanks. I'm not sure how this would help in my case. I'm not trying to do any phylogeny analysis. I just need to know if sequence I have was from one pure bacterial strain or from multiple strains.

Quote:
Originally Posted by GenoMax View Post
How to do this in practice: http://seqanswers.com/forums/showthread.php?t=16812

Analysis (see post #2) in this thread: http://seqanswers.com/forums/showthread.php?t=31565
shiningway is offline   Reply With Quote
Old 07-02-2013, 01:40 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,138
Default

Quote:
Originally Posted by shiningway View Post
Thanks. I'm not sure how this would help in my case. I'm not trying to do any phylogeny analysis. I just need to know if sequence I have was from one pure bacterial strain or from multiple strains.
My fault. The title on your original post made it sound (to me) like you were interested in identifying bacterial strains not specifically strains of the same species.

If the strains are expected to have small differences then this would be a difficult problem.

Last edited by GenoMax; 07-02-2013 at 01:43 PM.
GenoMax 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 11:39 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO