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 Similar Threads Thread Thread Starter Forum Replies Last Post ranjani Introductions 5 03-26-2013 07:53 PM bioinf Bioinformatics 8 10-14-2012 08:27 PM aloliveira Bioinformatics 1 04-05-2012 01:24 PM Newsbot! Literature Watch 0 03-17-2012 05:20 AM samanta General 2 08-02-2011 09:38 AM

 06-24-2013, 03:29 AM #1 anil KR Junior Member   Location: norway Join Date: Jan 2013 Posts: 8 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.
 06-24-2013, 03:51 AM #2 mastal Senior Member   Location: uk Join Date: Mar 2009 Posts: 667 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.
 06-24-2013, 03:54 AM #3 maasha Senior Member   Location: Denmark Join Date: Apr 2009 Posts: 153 The CLC explanation is nice and crisp: http://www.clcsupport.com/clcassembl..._it_works.html
 06-24-2013, 03:58 AM #4 anil KR Junior Member   Location: norway Join Date: Jan 2013 Posts: 8 Hi mastal, I have looked the paper previously but i didn't understand how the algorithms are working? Anil.
 06-24-2013, 04:05 AM #5 anil KR Junior Member   Location: norway Join Date: Jan 2013 Posts: 8 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.
 06-24-2013, 04:20 AM #6 GenoMax Senior Member   Location: East Coast USA Join Date: Feb 2008 Posts: 7,080 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
06-24-2013, 08:02 AM   #7
syfo
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Location: Southern EU

Join Date: Nov 2012
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Quote:
 Originally Posted by GenoMax 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)
This great article is available in open access here (pdf)

 06-24-2013, 08:49 AM #8 kadircaner Member   Location: Houston,TX Join Date: Jun 2011 Posts: 13 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
 06-25-2013, 12:33 AM #9 anil KR Junior Member   Location: norway Join Date: Jan 2013 Posts: 8 Thanks to Genomax,syfo and kadircaner the stuff is really useful. Thanks alot! Anil.