SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
de Bruijn graphs ranjani Introductions 5 03-26-2013 07:53 PM
Acquiring contigs, de Bruijn graphs, velvet bioinf Bioinformatics 8 10-14-2012 08:27 PM
Question on the de Bruijn Graphs aloliveira Bioinformatics 1 04-05-2012 01:24 PM
PubMed: Paired de bruijn graphs: a novel approach for incorporating mate pair informa Newsbot! Literature Watch 0 03-17-2012 05:20 AM
How do sequencing errors affect de Bruijn graphs? samanta General 2 08-02-2011 09:38 AM

Reply
 
Thread Tools
Old 06-24-2013, 03:29 AM   #1
anil KR
Junior Member
 
Location: norway

Join Date: Jan 2013
Posts: 8
Default De bruijn graphs

Hi,

Can anyone explain about the de Bruijn graph algorithms like how does it constructs the contigs from short read sequences? What i understood is that it constructs contigs basing on number of times the short reads ending with A,G,T,C . For instance , if a short read ending with A nucleotides are higher than the other short reads then it joins to the existing short read. This is how it constructs the contigs? Does ,this explaination is correct?

Thanks in Advance!

Anil.

Last edited by anil KR; 06-24-2013 at 03:41 AM.
anil KR is offline   Reply With Quote
Old 06-24-2013, 03:51 AM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default De bruijn graphs

Have a look at the velvet webpage

http://www.ebi.ac.uk/~zerbino/velvet/

Follow the links to the 2 velvet publications, they will explain how velvet works.
mastal is offline   Reply With Quote
Old 06-24-2013, 03:54 AM   #3
maasha
Senior Member
 
Location: Denmark

Join Date: Apr 2009
Posts: 153
Default

The CLC explanation is nice and crisp:

http://www.clcsupport.com/clcassembl..._it_works.html
maasha is offline   Reply With Quote
Old 06-24-2013, 03:58 AM   #4
anil KR
Junior Member
 
Location: norway

Join Date: Jan 2013
Posts: 8
Default

Hi mastal,

I have looked the paper previously but i didn't understand how the algorithms are working?


Anil.
anil KR is offline   Reply With Quote
Old 06-24-2013, 04:05 AM   #5
anil KR
Junior Member
 
Location: norway

Join Date: Jan 2013
Posts: 8
Default

Hi,


Thanks to mastal and maasha for the links. i am looking into it and seems it would be helpful for understanding the graphs.

Anil.
anil KR is offline   Reply With Quote
Old 06-24-2013, 04:20 AM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,080
Default

Nature biotechnology has a good article: http://www.nature.com/nbt/journal/v2.../nbt.2023.html

If you do not have access to an online subscription then here is the reference : Nature Biotechnology, Vol 29, 987–991 (2011)

Last edited by GenoMax; 06-28-2013 at 12:00 PM. Reason: Corrected link
GenoMax is offline   Reply With Quote
Old 06-24-2013, 08:02 AM   #7
syfo
Just a member
 
Location: Southern EU

Join Date: Nov 2012
Posts: 103
Default

Quote:
Originally Posted by GenoMax View Post
Nature biotechnology has a good article: http://www.nature.com/nbt/journal/v2.../nbt.2023.html

If you do not have access to an online subscription then here is the reference : Nature Biotechnology, Vol 29, 987991 (2011)
This great article is available in open access here (pdf)
syfo is offline   Reply With Quote
Old 06-24-2013, 08:49 AM   #8
kadircaner
Member
 
Location: Houston,TX

Join Date: Jun 2011
Posts: 13
Default

I think following is one of the best tutorials I've seen so far:
http://www.homolog.us/Tutorials/index.php?p=1.1&s=1
kadircaner is offline   Reply With Quote
Old 06-25-2013, 12:33 AM   #9
anil KR
Junior Member
 
Location: norway

Join Date: Jan 2013
Posts: 8
Default

Thanks to Genomax,syfo and kadircaner the stuff is really useful.


Thanks alot!

Anil.
anil KR 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 06:21 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO