DETAILS ABOUT PARALLEL MOTIF FINDING ALGORITHMS FOR BIOINFORMATICS

WMU CS6260 Parallel Computations II Spring 2013 Presentation #2Professor: Dr. de DonckerName: Xuanyu Hu March/11/2013

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

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Quick Review About Last Presentation More Details

Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

QUICK REVIEW- SEQUENCING DNA

Pattern in DNA Function Drug target identification and new drug

discovery

REVIEW - GENE MUTATION

REVIEW - SOLUTION

Solution in a Sequential Way Greedy Algorithm Brute Force Branch And Bound

Parallelize the serial program with MPI Loading balance in parallel program

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

THE BEGINNING OF BIOINFORMATICS

Over the past decade there has been a dramatic increase in the number of completely sequenced genomes resulting from the race of multibillion-dollar genome-sequencing projects.

GENBANK

The results of these achievements have led to a flood of data in genome sequence databases such as Genbank and EMBL, which has caused them to double in size almost every year.

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

THE BEGINNING OF BIOINFORMATICS

This flood of sequence data requires a system of representing, organising, manipulating, distributing, maintaining and finally using the information (Computer Simulation).

Bioinformatics(bridge) Computer Science work with Biology Computer Science work for Biology

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

HOW TO USE GENBANK

HOW TO USE GENBANK

Example: Protein consensus pattern to DNA RegEx

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

PROBLEMS More and more DNA

sequence Not enough memory for

DNA sequence If we don’t have the

super-computer with lots of processors Can I find the results with

normal computers with the same performance of parallel computation?

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

60 MB GENOME FILE: CHROMO20.FA

250 MB GENOME FILE: CHROMO1.FA

1072 MB GENOME FILE: CHROMO1-5.FA

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

THE RESULTS OF OUR PROJECT

1 2 3 4 5 6 7 8 90

2

4

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#Processes

Tim

e (

Secs.)

N = 55, T = 20, L = 9

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

FUTURE(SOLUTION FOR PROBLEMS)

A far more practical and effective approach incorporates the usage of parallel clusters of workstations.

Cloud Computing

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

CONCLUSION

Details about Parallel Motif Finding Algorithms for Bioinformatics Quick Review About Last Presentation More Details

Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future(Solution for problems)

Download Transformation Find the Pattern Bioinformatics give the information biologists need

THANK YOU FOR LISTENING

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

NOTHING IS IMPOSSIBLE

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

QUESTIONS?

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Genbank The Beginning Of Bioinformatics How to use genbank Problems

Good Performance In Bioinformatics The Results From Real DNA The Results Of Our Project Future

Conclusion Nothing Is Impossible Questions References

REFERENCE

http://eprints.ru.ac.za/162/1/Akhurst_MSc.pdf

http://www.ncbi.nlm.nih.gov/gene/