SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
primer design razibus General 6 12-05-2014 05:04 AM
Primer design for unidirectional sequencing soleulloa 454 Pyrosequencing 12 10-03-2011 04:52 AM
HELP, primer design problem in gap closure f0415007 General 1 09-28-2011 02:44 AM
HELP, primer design problem in gap closure f0415007 Illumina/Solexa 0 09-20-2011 11:46 PM
PCR Primer Design Software for Gap-closure bulletin2007 454 Pyrosequencing 5 05-19-2010 11:58 AM

Reply
 
Thread Tools
Old 01-17-2011, 11:36 PM   #1
fungs
Member
 
Location: DE/SE

Join Date: Jan 2010
Posts: 10
Default Primer design reference positions

Hello,
this might seem like a very basic question but I could not find a clear answer, yet. So I am hoping that anyone here is familiar with this matter.

I'm dealing with 16S primers for hypervariable regions. There are some primer variants like '967F' that are published in literature and used to amplify these regions. I know that positions are usually given in terms of E.coli genome positions. This would mean that the Primer 5' start position is at the 967th base of the corresponding reference E.coli 16S rRNA gene? Then, I would like to know which E.coli genome and which rRNA copy in the genome is specifically taken as reference. There are so many E.coli sequences in public databases...

Yes, I could probably align the primers to any of the reference sequences but I would like to know the definition.

Thanks for your help, if you happen to know.

J.
fungs is offline   Reply With Quote
Old 02-26-2013, 02:37 PM   #2
nmcnulty
Junior Member
 
Location: St. Louis

Join Date: Feb 2013
Posts: 1
Default Primer design reference positions

I found your post while searching around for an answer to the same question. After a fair bit of digging, I found some articles suggesting that the E. coli 16S numbering scheme is based on the sequence reported by Brosius et al. in PNAS in 1978:

http://www.pnas.org/content/75/10/48...e2=tf_ipsecsha

For completeness, here is one of the articles claiming this is the scheme used:

http://www.ncbi.nlm.nih.gov/pmc/arti...00311-0162.pdf
nmcnulty is offline   Reply With Quote
Old 12-04-2018, 02:00 AM   #3
fungs
Member
 
Location: DE/SE

Join Date: Jan 2010
Posts: 10
Default Thx

Never thanked you for your answer. Thx!
fungs 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 06:11 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO