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Cluster Computer For Bioinformatics Applications

Nile University, Bioinformatics Group. Cluster Computer For Bioinformatics Applications. Hisham Adel 2008. Done By:. Hisham Adel Hassan. Supervised by: Dr. Mohamed Aboualhouda. Points. Introduction. Cluster and Supercomputers. Cluster Types and Advantages. Our Cluster.

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Cluster Computer For Bioinformatics Applications

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  1. Nile University, Bioinformatics Group. Cluster Computer For Bioinformatics Applications Hisham Adel 2008

  2. Done By: Hisham Adel Hassan. Supervised by: Dr. Mohamed Aboualhouda

  3. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance. • Cluster Computer for Basic Problems. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  4. Introduction

  5. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance. • Cluster Computer for Basic Problems. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  6. Cluster Definition • Group of computers and servers (connected together) that act like a single system. • Each system called a Node. • Node contain one or more Processor , Ram ,Hard disk and LAN card. • Nodes work in Parallel. • We can increase performance by adding more Nodes.

  7. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance. • Cluster Computer for Basic Problems. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  8. Cluster types • Load Balancing Cluster (Parallel BLAST). • Computing Cluster(Parallel sequence alignment). • High-availability (HA) clusters.

  9. Cluster types:Load Balancing Cluster Task

  10. Cluster types:Computing Cluster Task

  11. Cluster type:High-availability Clusters

  12. Cluster advantages • Performance. • Scalability. • Maintenance. • Cost.

  13. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance. • Cluster Computer for Basic Problems. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  14. Our Cluster Node 4 Node 1 Internet Internet switch Node 3 Node 2 Internet Internet

  15. Our Cluster specification Communication : Switch 5-Port 10/100Mbps. Processor and Ram: -Master Node Duo core Processor 1.86 GHZ. Ram 1GB. -Node 1 Pentium 4 Ram 1GB. -Node 2 Pentium 4 Ram 1GB -Node 3 Pentium 4 Ram 512 MB

  16. Our Cluster specification (cont’)‏ • Operating System OPEN SUSE 10.3 http://software.opensuse.org/ • MPICH2 http://www.mcs.anl.gov/research/projects/mpich2/

  17. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance. • Cluster Computer for Basic Problems. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  18. Performance of the Cluster is affected by 1-Node speed. 2-Running Program.

  19. Running Program(sequential)‏ Working…

  20. Running Program(sequential)‏ Working…

  21. Running Program(sequential)‏ Working…

  22. Running Program(sequential)‏

  23. Running Program(Parallel)‏ Data sent Data sent Data sent

  24. Running Program(Parallel)‏ Working… Working… Working… Working…

  25. Running Program(Parallel)‏ Finished… Results Get results… Finished… Results Finished… Results

  26. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance. • Cluster Computer for Basic Problems. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  27. Sequence Alignment

  28. Sequence Alignment Used to : 1-Compare between sequences. 2-Search databases.

  29. How to Align two Sequences. if we have two sequences A A A C G A A A T G A Let match=1, gap=-1 , miss-match=0. they can be aligned as: 1- A A A C G A | | | | | | Score=3 A A T _ G A 2- A A A C _ G A | | | | | | | Score=1 A A _ _ T G A

  30. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance • Cluster Computer for Basic Problems.. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  31. BLAST (Basic Local Alignment Search Tool)‏ Searching DataBases

  32. BLAST Algorithm (High scoring pairs)‏

  33. Blast search types. BLASTN -Compares a nucleotide query sequence against a nucleotide sequence database. BLASTP- Compares an amino acid query sequence against a protein sequence database. TBLASTN- Compares a protein query sequence against a nucleotide sequence Database. BLASTX- Compares nucleotide query sequence against a protein sequence database.

  34. Why We need BLAST to be parallelized ?

  35. Our Program:Parallel BLAST

  36. Parallel BLAST(cont’)‏ Formatdb.c Nucleotide sequence database “formatdb -i DATABASE -p F “. Protein sequence database “formatdb -i DATABASE -p T “.

  37. Parallel BLAST(cont’)‏ Linux_Cluster_BLASTALL.c “blastall -p BLAST Search Type -d DATABASE -i QUERY FILE -o out . Txt”

  38. Results Average of running 1000 Query, 1000 times.

  39. Results(cont’)‏ Average of running 1000 Query, 1000 times.

  40. Results(cont’)‏ Average of running 1000 Query, 1000 times.

  41. Conclusion about Parallel BLAST. • Performane: Batter by using CLUSTER. • Scalability:More Nodes time decrease.

  42. Points • Introduction. • Cluster and Supercomputers. • Cluster Types and Advantages. • Our Cluster. • Cluster Performance. • Cluster Computer for Basic Problems. • General Idea about Sequence Alignment. • BLAST and Parallel BLAST Algorithm. • Sequence Alignment and Parallel Sequence Alignment. • Learned Skills.

  43. Sequence Alignment Compare between sequences

  44. Sequence Alignment • Introduction. • Sequence Alignment Benefits. • Sequence Alignment Types.

  45. Needleman-Wunsch Algorithm

  46. Why We need Sequence Alignment to be parallelized ?

  47. Parallel Sequence Alignment algorithm

  48. Our Sequence Alignment Program • Pairwise Alignment. • Built Using Needleman-Wunsch algorithm.

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