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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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slide1

Nile University,

Bioinformatics Group.

Cluster Computer For Bioinformatics Applications

Hisham Adel

2008

slide2

Done By:

Hisham Adel Hassan.

Supervised by:

Dr. Mohamed Aboualhouda

slide3

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.
slide5

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.
slide6

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.
slide9

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.
slide10

Cluster types

  • Load Balancing Cluster (Parallel BLAST).
  • Computing Cluster(Parallel sequence alignment).
  • High-availability (HA) clusters.
slide14

Cluster advantages

  • Performance.
  • Scalability.
  • Maintenance.
  • Cost.
slide15

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.
slide16

Our Cluster

Node 4

Node 1

Internet

Internet

switch

Node 3

Node 2

Internet

Internet

slide17

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

slide18

Our Cluster specification (cont’)‏

  • Operating System OPEN SUSE 10.3

http://software.opensuse.org/

  • MPICH2

http://www.mcs.anl.gov/research/projects/mpich2/

slide19

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.
slide20

Performance of the Cluster is affected by

1-Node speed.

2-Running Program.

slide25

Running Program(Parallel)‏

Data sent

Data sent

Data sent

slide26

Running Program(Parallel)‏

Working…

Working…

Working…

Working…

slide27

Running Program(Parallel)‏

Finished…

Results

Get results…

Finished…

Results

Finished…

Results

slide28

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.
slide30

Sequence Alignment

Used to :

1-Compare between sequences.

2-Search databases.

slide31

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

slide32

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.
slide33

BLAST

(Basic Local Alignment Search Tool)‏

Searching DataBases

slide34

BLAST Algorithm

(High scoring pairs)‏

slide35

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.

slide38

Parallel BLAST(cont’)‏

Formatdb.c

Nucleotide sequence database “formatdb -i DATABASE -p F “.

Protein sequence database “formatdb -i DATABASE -p T “.

slide39

Parallel BLAST(cont’)‏

Linux_Cluster_BLASTALL.c

“blastall -p BLAST Search Type -d DATABASE -i QUERY FILE -o out . Txt”

slide40

Results

Average of running 1000 Query, 1000 times.

slide41

Results(cont’)‏

Average of running 1000 Query, 1000 times.

slide42

Results(cont’)‏

Average of running 1000 Query, 1000 times.

slide43

Conclusion about Parallel BLAST.

  • Performane: Batter by using CLUSTER.
  • Scalability:More Nodes time decrease.
slide44

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.
slide45

Sequence Alignment

Compare between sequences

slide46

Sequence Alignment

  • Introduction.
  • Sequence Alignment Benefits.
  • Sequence Alignment Types.
slide50

Our Sequence Alignment Program

  • Pairwise Alignment.
  • Built Using Needleman-Wunsch algorithm.
slide51

Learned Skills.

  • Using Linux (Suse 10.3) operating system.
  • Programming using C language.
  • Cluster computers and how to build one.
  • MPICH2 for message passing interfaces between nodes.
  • Latex.
  • Team working, and helping each other.
  • Presentation skills.