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
