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From "Tsz Wo \(Nicholas\), Sze" <s29752-hadoopu...@yahoo.com>
Subject Re: Hadoop for Bioinformatics
Date Tue, 29 Mar 2011 17:51:08 GMT
Hi Franco,

I recall that there are some Hadoop-Blast researches/projects.  For examples, 
see


- http://www.cs.umd.edu/Grad/scholarlypapers/papers/MichaelSchatz.pdf
- http://salsahpc.indiana.edu/tutorial/hadoopblast.html

Nicholas



________________________________
From: Franco Nazareno <franco.nazareno@gmail.com>
To: common-user@hadoop.apache.org
Sent: Sun, March 27, 2011 7:51:14 PM
Subject: Hadoop for Bioinformatics

Good day everyone!



First, I want to congratulate the group for this wonderful project. It did
open up new ideas and solutions in computing and technology-wise. I'm
excited to learn more about it and discover possibilities using Hadoop and
its components. 



Well I just want to ask this with regards to my study. Currently I'm
studying my PhD course in Bioinformatics, and my question is that can you
give me a (rough) idea if it's possible to use Hadoop cluster in achieving a
DNA sequence alignment? My basic idea for this goes something like a string
search out of a huge data files stored in HDFS, and the application uses
MapReduce in searching and computing. As the Hadoop paradigm impies, it
doesn't serve well in interactive applications, and I think this kind of
searching is a "write-once, read-many" application.



I hope you don't mind my question. And it'll be great hearing your comments
or suggestions about this.



Thanks and more power!

Franco
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