Running BLAST on the cluster system over the Pacific Rim.

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Presentation transcript:

Running BLAST on the cluster system over the Pacific Rim

What is BLAST? A DNA and Protein sequence/database alignment tool Developed by NCBI (National Center for Biotechnology Information), US. Throughput is the key issue of providing service Running in single machine  Not scalable  Low throughput  Unable to handle large dataset

The challenges of large genomic sequence alignment Problem Complexity – O(NxM)  N: Query (DNA) size  M: Database (EST/Protein DB) size Limited computing power Limited data storage Database sharing Private data protection

BLAST goes into parallel - mpiBLAST A parallel BLAST runs in single cluster Developed by Los Alamos National Lab. Splitting large database into small fragments Performing master-worker scheme of job running

mpiBLAST Advantages  High throughput  Load Balancing Running in local cluster  Performance and Problem size still be limited by local computing power  Simultaneous I/O to centralized database causes the performance bottleneck  Database sharing is still difficult

BLAST goes into Grid – mpiBLAST-g2 A parallel BLAST runs on Grid The enhancement from mpiBLAST by ASCC Using GT2 GASSCOPY API and MPICH-g2 Performing cross cluster scheme of job execution Performing remote database sharing

mpiBLAST-g2

Advantages of mpiBLAST-g2 Sharing idle resources in Virtual Organization (VO)  Solving problems larger than before Fetching database from remote site in secured mode  Reducing the load of local database server  Protecting private data Providing tools for database replication  Simplifying the management work

Grid resources Resources are from PRAGMA  ASCC, Taiwan  AIST, Japan  BII, Singapore  KISTI, Korea  SDSC, U.S.

Grid Resources kISTI

Demonstration cases Query – Arabidopsis Chr4 contig (600 Kbps) Database – Arabidopsis cDNA (~50 Mbps)

Thanks for your attention!

Testing results