SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ArXiv: Optimal Assembly for High Throughput Shotgun Sequencing krobison De novo discovery 0 01-03-2013 09:43 AM
Can smRNA sequencing primer and genomic DNA sequencing primer mixed in one lane? whimsy Illumina/Solexa 3 04-06-2011 10:30 AM
PubMed: Methods for generating shotgun and mixed shotgun/paired-end libraries for the Newsbot! Literature Watch 0 04-11-2009 06:40 AM

Reply
 
Thread Tools
Old 07-28-2013, 04:42 PM   #1
arkilis
Senior Member
 
Location: Australia

Join Date: Jul 2013
Posts: 119
Post new to bio: Can primer walking only be used in Shotgun sequencing?

When I was reading paper "Primer walking has become widely used as a means of
closing the gaps left after shotgun sequencing of large
insert clones." I was thinking is the primer walking can only be used after shotgun sequencing?

Thanks

Paper "Primer walking" From Primer Walking
Eugene Sverdlov, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry,
Russian Academy of Sciences, Moscow, Russia
Tatyana Azhikina, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian
Academy of Sciences, Moscow, Russia
arkilis is offline   Reply With Quote
Old 07-29-2013, 01:36 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

You can use primer walking to sequence pretty much any long unknown sequence. You're likely to use it after shotgun sequencing since you're often left with gaps, but you could certainly use it for other things.
dpryan is offline   Reply With Quote
Old 07-29-2013, 06:03 AM   #3
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

Conversely, primer walking is a much more expensive & slow approach than shotgun sequencing, so it makes sense to shotgun first & then finish off with primer walks. True primer walking is becoming uncommon as modern shotgun sequencing techniques can frequently give very highly connected scaffolds, so primers may be used for polishing or gap closing but actual walks are minimized.
krobison is offline   Reply With Quote
Old 07-29-2013, 11:20 PM   #4
arkilis
Senior Member
 
Location: Australia

Join Date: Jul 2013
Posts: 119
Default

Quote:
Originally Posted by krobison View Post
Conversely, primer walking is a much more expensive & slow approach than shotgun sequencing, so it makes sense to shotgun first & then finish off with primer walks. True primer walking is becoming uncommon as modern shotgun sequencing techniques can frequently give very highly connected scaffolds, so primers may be used for polishing or gap closing but actual walks are minimized.

Make much more sense to me! Thank you
arkilis is offline   Reply With Quote
Old 07-30-2013, 12:32 AM   #5
arkilis
Senior Member
 
Location: Australia

Join Date: Jul 2013
Posts: 119
Default

Quote:
Originally Posted by dpryan View Post
You can use primer walking to sequence pretty much any long unknown sequence. You're likely to use it after shotgun sequencing since you're often left with gaps, but you could certainly use it for other things.
Very Clear~ thanks, it helps a lot
arkilis is offline   Reply With Quote
Reply

Tags
primer walking

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 01:35 AM.


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