IMPLEMENTATION OF SEED ALGORITHM FOR DNA

SEQUENCE COMPARISON ON FPGA PLATFORM

Under the guidance of:- By:-

Mr. Rajesh Mehra ( Assistant Sonali Vijan
Professor) ME (ECE) Regular
ECE Department
OUTLINES
q OVERVIEW
§ INTRODUCTION
q LITERATURE SURVEY
§ EXISTING CHALLANGES
q PROPOSED WORK OBJECTIVE
q DESIGN METHODOLOGY
q EXPECTED OUTCOME
q TIME PLAN
q REFERENCES


§
OVERVIEW
BIOINFORMATICS
HUMAN GENOME
Ø The genome is entirely an organism’s hereditary information.


Ø Genes carry information for making all the proteins required by

body for growth and maintainence.


Ø It is encoded either in DNA or in RNA.

HUMAN GENOME PROJECT (GOALS)

Identify all the genes in human DNA

store the information in the database

To develop faster, more efficient sequencing technologies

Develop tools for data analysis

IMPLEMENTATION ON FPGA
LITERATURE SURVEY

CONCLUSION:- Computation is improved by a factor of 19.

GN scope accelerator achieved a speed up of 383.4 and DIALIGN allignment accelerator re
about 4 times is achieved over the software run on a modern general purpose compute
CONCLUSION:- Speed up compared to BLAST range from 5 to 28.
LITERATURE SURVEY REMARKS
EXISTING CHALLENGES
PROPOSED WORK OBJECTIVE

objectiv Scope of
e research work
To implement To increase the
seed algorithm for speed of the
intensive DNA algorithm for faster
sequence genomic sequence
comparison on comparisons.
FPGA platform.
DESIGN METHODOLOGY
EXPECTED OUTCOME
TIME PLAN
REFERENCES
• A. Jacob, J. Lancaster, J. Buhler, and R. D. Chamberlain. “Fpga-accelerated seed generation in mercury
blastp,” in FCCM ’07: Proceedings of the 15th Annual IEEE Symposium on Field-Programmable
Custom Computing Machines, pages 95–106, 2007.
• E. Sotiriades and A. Dollas, “Design space exploration for the blast algorithm implementation,” in FCCM
’07: Proceedings of the 15th Annual IEEE Symposium on Field- Programmable Custom Computing
Machines, pages 323– 326, 2007.
• A. A. Mendon and R. Sass. “A Hardware Filesystem Implementation for High-Speed Secondary Storage,”
in Proceedings of the 2008 International Conference on Reconfigurable Computing and FPGAs, Dec
2008.
• K. Muriki, K. D. Underwood, and R. Sass. “Rc-blast: Towards a portable, cost-effective open source
hardware implementation,” in IPDPS ’05: Proceedings of the 19th IEEE International Parallel and
Distributed Processing Symposium (IPDPS’05) - Workshop 7, page 196.2, 2005.
• K. Puttegowda, W. Worek, N. Pappas, A. Dandapani, and P. Athanas, “A Run-Time Reconfigurable
System for Gene-Sequence Searching,” Proc. Int’l Conf. VLSI Design, pp. 561-566, 2003.
• A. Marongiu, P. Palazzari, and V. Rosato, “A Specialized Hardware Device for the Protein Similarity
Search,” Concurrency and Computation: Practice and Experience, vol. 16, pp. 917-931, 2004.
• T.F. Oliver, B. Schmidt, and D.L. Maskell, “Hyper Customized Processors for Bio-Sequence Database
Scanning on FPGAs,” Proc. ACM/SIDA Int’l Conf. Field Programmable Gate Arrays, pp. 229-237, 2005.
• A. Di Bias et al., “The UCSC Kestrel Parallel Processor,” IEEE Trans. Parallel and Distributed Systems,
vol. 16, no. 1, pp. 80-92, Jan. 2005.
.


•
• P. Zhang, G. Tan, and G.R. Gao, “Implementation of the Smith- Waterman Algorithm on a Reconfigurable
Supercomputing Platform,” Proc. Int’l Conf. High Performance Networking and Computing, pp. 39-48,
2007.
• X. Jiang, X. Liu, L. Xu, P. Zhang, and N. Sun, “A Reconfigurable Accelerator for Smith-Waterman
Algorithm,” IEEE Trans. Circuits and Systems II, vol. 54, no. 12, pp. 1077-1081, Dec. 2007.
• B. Harris, A.C. Jacob, J.M. Lancaster, J. Buhler, and T.D. Chamberlain, “A Banded Smith-Waterman
FPGA Accelerator for Mercury BlastP,” Proc. Int’l Conf. Field Programmable Logic and Applications,
pp. 765-769, 2007.
• Silicon Graphics Inc., “SGI Reconfigurable Application Specific Computing: Accelerating Production
Workflows,” White paper, www.sgi.com/pdfs/3721.pdf., 2006.
• S.Y. Kung et al., “Wavefront Array Processors—Concept to Implementation,” Computer, vol. 20, no. 7, pp.
18-33, July 1987.
• [33] J. Lee, V. Narayanan, M.J. Irwin, and W. Wolf, “An Efficient Architecture for Motion Estimation and
Compensation in the Transform Domain,” IEEE Trans. Circuits and Systems for Video Technology, vol.
16, no. 2, pp. 191-201, Feb. 2006.
• K. Muriki, K.D. Underwood, R. Sass, RC-BLAST: Towards a Portable, Cost-Effective Open Source
Hardware Implementation, In proc. IPDPS 2005: Fourth IEEE International Workshop on High
Performance Computational Biology, Denver, CO, April 4, 2005.
 

 THANK YOU

Today’s Presenters

John Adam
Managing Tom Jacob Bill Nova
Director Director IT DB Consultant
Global Global Global
Associates Associates Associates

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Table of contents

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Organizational Chart

CEO

VP IT VP Admin Secretary

Manager Development Manager Admin

Accounts
&
Manager QA Manager HR Finance Staff

Test Lead 1 Dev Lead 1 Admin Officer 1

Team Members Team Members HR Executive 1
Admin Officer 2
List List HR Executive 2
Support 1
HR Support 1
Test Lead 2 Dev Lead 2 Support 2
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Team Members List Team Members List Support 3

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Area Wise Distribution

90
80
70
60
50 East
40 West
30 North
20
10
0
1st Qtr 2nd Qtr 3rd Qtr 4th Qtr
Quarterly Sale

13% 13%

17% 1st Qtr

2nd Qtr
3rd Qtr
4th Qtr

57%
Employee Detail

Employee No Name Gender Grade Department

70899 Triet Beo Male 4 Management

70909 David Smith Male 4 Marketing

70839 Susan Cyler Female 4 Dev

70800 Suzi Decosa Female 5 Management

70829 Abrahim Bukhatir Male 2 Dev

70394 Suresh Kumar Male 5 Dev

70291 Deborah Green Female 3 Testing

70844 Michael Bennot Male 1 Doc

70194 George Wood Male 2 Testing

Area Wise Growth

180
160
140
120
100 North
West
80
East
60
40
20
0
1st Qtr 2nd Qtr 3rd Qtr 4th Qtr
Important Points

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Project Iterations

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Main Points

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Timeline

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Economic Growth Circular Flow Model

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Checklist

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