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Re: Hadoop for Bioinformatics
On March 28, 2011 04:51:14 Franco Nazareno wrote:
>
> 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'll add some relevant citations:

An overview of the Hadoop/MapReduce/HBase framework and its current
applications in bioinformatics
http://www.biomedcentral.com/1471-2105/11/S12/S1
Biodoop: Bioinformatics on Hadoop
http://www.computer.org/portal/web/csdl/doi/10.1109/ICPPW.2009.37
CloudBurst: highly sensitive read mapping with MapReduce
http://bioinformatics.oxfordjournals.org/content/25/11/1363.short
CloudBLAST: Combining MapReduce and Virtualization on Distributed Resources
for Bioinformatics Applications
http://www.computer.org/portal/web/csdl/doi/10.1109/eScience.2008.62
--
Luca Pireddu
CRS4 - Distributed Computing Group
Loc. Pixina Manna Edificio 1
Pula 09010 (CA), Italy
Tel:  +39 0709250452
NEW: Monitor These Apps!
elasticsearch, apache solr, apache hbase, hadoop, redis, casssandra, amazon cloudwatch, mysql, memcached, apache kafka, apache zookeeper, apache storm, ubuntu, centOS, red hat, debian, puppet labs, java, senseiDB