- Sofia Breschi, B.Sc. student in Biomedical Engineering - Beatrice Branchini, B.Sc. student in Biomedical Engineering In the last few years, the use of Next Generation Sequencing technology in medicine has become more and more common, in particular for the diagnosis of genetic diseases and the production of personalized drugs. In this context, the identification of characteristic patterns in the human genome plays an important role. Exact pattern matching algorithms are an efficient way to identify those sequences. However, this process represents a bottleneck in the genomic field as it is very computationally intensive and time-consuming. Moreover, general-purpose architectures are not optimized to handle the huge amount of data and operations used in a genomics context. Due to these considerations, we propose an implementation of the Knuth-Morris-Pratt (KMP) algorithm on FPGA, a particular family of integrated circuits capable of reconfiguration for an infinite number of times. The KMP algorithm results in being very fast and efficient, by reducing unnecessary comparisons of characters that have already been matched. Furthermore, to achieve an overall speedup of the alignment process, the implementation on FPGA will bring on an even faster and more efficient solution, thus providing the patient with a quick response.

1. Maeve
Fast genome analysis leveraging
exact string matching
Beatrice Branchini <beatrice.branchini@mail.polimi.it>
Sofia Breschi <sofia.breschi@mail.polimi.it>
Alberto Zeni <alberto.zeni@mail.polimi.it>
Marco Santambrogio <marco.santambrogio@polimi.it>
July 22, vNGC

2. Genomics investigation
2

3. Applications
Diagnosis of genetic diseases
Personalized medicine
3
Prevention of diseases

4. https://www.genome.gov/sequencingcostsdata
4
Genome analysis cost
DNA sequencing cost per genome

5. Sequencing Assembly
Genomic pipeline
5
DNA analysis

6. Sequencing
Genomic pipeline
6
DNA analysisAssembly

7. Context
Exact pattern
matching algorithms
7

8. Technical challenges
8
Computationally intensive
Time consuming
Inefficient architectures

9. Solution
9
Implementation of
Knuth-Morris-Pratt (KMP) algorithm
on FPGA

10. KMP algorithm
10
• linear time complexity
KMP is an exact pattern matching algorithm
• reduces unnecessary comparisons of
characters

11. Solution
11
Implementation of
Knuth-Morris-Pratt (KMP) algorithm
on FPGA
KMP fast and efficient
FPGA acceleration FPGA

12. Our implementation
12
Genome
+
SEQ1
Genome
+
SEQ2
Genome
+
SEQ3
Genome
+
SEQ4

13. Our implementation
13
Genome
+
SEQ1
Genome
+
SEQ2
Genome
+
SEQ3
Genome
+
SEQ4
Failure table
for SEQ1
Failure table
for SEQ4
Failure table
for SEQ3
Failure table
for SEQ2

14. Our implementation
14
Genome
+
SEQ1
Genome
+
SEQ2
Genome
+
SEQ3
Genome
+
SEQ4
Failure table
for SEQ1
Failure table
for SEQ4
Failure table
for SEQ3
Failure table
for SEQ2
Matching
Matching
Matching
Matching

15. Our implementation
15
Genome
+
SEQ1
Genome
+
SEQ2
Genome
+
SEQ3
Genome
+
SEQ4
Match/
mismatch
Match/
mismatch
Match/
mismatch
Match/
mismatch
Failure table
for SEQ1
Failure table
for SEQ4
Failure table
for SEQ3
Failure table
for SEQ2
Matching
Matching
Matching
Matching

16. Results
16
~ 6x improvement
over multicore
Overall speedup of the alignment process
Board: Xilinx Alveo U200
Software: Vitis

17. Thanks for
your attention
Beatrice Branchini <beatrice.branchini@mail.polimi.it>
Sofia Breschi <sofia.breschi@mail.polimi.it>
Alberto Zeni <alberto.zeni@mail.polimi.it>
Marco Santambrogio <marco.santambrogio@polimi.it>