gratus907 / FMHE

Compressed/Searchable Index and Genome Analysis with Homomorphic Encryption

Compressed/Searchable Index and Genome Analysis with Homomorphic Encryption

(1) FM-index of Alignment

Stored in FMA directory.

Requirements

Succinct Data Structures Library 2.0 (SDSL)

Installation

To complie, set SDSL_DIR in the makefile to point to your SDSL directory.

git clone https://github.com/SNUCSE-CTA/FMHE
cd FMHE/FMA
make all

Running example in [4]

Build FM-index of alignment
Set saa_dens and isaa_dens in buildFMA.cpp, locate.cpp, and extract.cpp same as sampling_rate of SAA. (default: 32)

mkdir example/output

#./buildSAA sampling_rate reference_file vcf_file output_directory [num_threads]
./buildSAA 32 example/example_reference example/example.vcf ./example/output/ 8

#./buildFMA saa_directory num_strings output_directory
./buildFMA ./example/output/ 4 ./example/output/

Locate

#./locate saa_directory fma_directory num_strings pattern_file
./locate ./example/output/ ./example/output/ 4 ./example/locate_example.txt > ./example/output/result_locate.txt

Extract

#./extract saa_directory fma_directory num_strings pattern_file pattern_size
./extract ./example/output/ ./example/output/ 4 ./example/extract_example.txt 4 > ./example/output/result_extract.txt

Data

chr1.tar.gz (61MB)
3.chr1.vcf.tar.gz (20MB)
100.chr1.vcf.tar.gz (495MB)
250.chr1.vcf.tar.gz (1.5GB)
500.chr1.vcf.tar.gz (3.8GB)
locate pattern
extract pattern

References

[1] Joong Chae Na, Heejin Park, Maxime Crochemore, Jan Holub, Costas S. Iliopoulos, Laurent Mouchard, and Kunsoo Park. Suffix tree of alignment: An efficient index for similar data, In International Workshop on Combinatorial Algorithms, 8288:337-348, Springer, Berlin, Heidelberg, 2013. DOI: 10.1007/978-3-642-45278-9_29

[2] Joong Chae Na, Heejin Park, Sunho Lee, Minsung Hong, Thierry Lecroq, Laurent Mouchard, and Kunsoo Park. Suffix array of alignment: A practical index for similar data, In International Symposium on String Processing and Information Retrieval, 8214:243-254, Springer, Cham, 2013. DOI: 10.1007/978-3-319-02432-5_27

[3] Joong Chae Na, Hyunjoon Kim, Heejin Park, Thierry Lecroq, Martine Léonard, Laurent Mouchard, and Kunsoo Park. FM-index of alignment: A compressed index for similar strings, Theoretical Computer Science 638:159-170, 2016. DOI: 10.1016/j.tcs.2015.08.008

[4] Joong Chae Na, Hyunjoon Kim, Seunghwan Min, Heejin Park, Thierry Lecroq, Martine Léonard, Laurent Mouchard, and Kunsoo Park. FM-index of alignment with gaps, Theoretical Computer Science 710:148-157, 2018. DOI: 10.1016/j.tcs.2017.02.020

(2) Homomorphic Computation of Local Alignment

A tool that computes optimal and approximate local alignments between two encrypted genomic sequences with affine gap penalty.
Stored in HLA directory.

Requirements

OpenMP
TFHE
HEaan.STAT
Python 3

Run

python3 homla.py (app|opt) inputFileX inputFileY [reflen] [--scheme M,S,Go,Ge] [--lib (TFHE|HEAAN)]

M-Match score, S-Mismatch score, Go-Gap opening penalty, and Ge-Gap extending penalty.

Default parameter

HE scheme: TFHE
Scoring scheme: 5/-3, -9, -1

Sample input

For optimal local alignment: x.fasta, y.fasta
For approximate local alignment: x.vcf, y.vcf

Sample run

Compute optimal local alignment:

python3 homla.py opt x.fasta y.fasta --scheme 5,-3,-9,-1

Output:

Scoring scheme: 5/-3, -9, -1
Input: x.fasta y.fasta
Lengths : 7 9
Encryption time: 1.01s
Homomorphically evaluating alignment...
Homomorphic computation time: 80.64s
Decryption time: 0.43s
RESULT
------------------
Score: 11
Starting pos: 2 3
Ending pos: 5 7

Compute approximate local alignment:

python3 homla.py app x.vcf y.vcf 26 --scheme 5,-3,-9,-1 --lib TFHE

Output:

Scoring scheme: 5/-3, -9, -1
Input: x.vcf y.vcf
Number of varaints: 5
Length of Reference Genome: 26
Encryption time: 1.04s
Homomorphically computing alignment...
Homomorphic computation time: 31.30s
Decryption time: 0.29s
RESULT
------------------
Score: 33
Starting pos: 5
Ending pos: 16

Or

python3 homla.py app x.vcf y.vcf 26 --scheme 5,-3,-9,-1 --lib HEAAN

Output:

Scoring scheme: 5/-3, -9, -1
Input: x.vcf y.vcf
Number of varaints: 5
Length of Reference Genome: 26
Encryption time: 3.54s
Homomorphically computing alignment...
Homomorphic computation time: 623.59s
Decryption time: 0.06s
RESULT
------------------
Score: 32.82

References

[1] M. Bataa, S. Song, K. Park, M. Kim, J.H. Cheon, and S. Kim. Homomorphic Computation of Local Alignment, Proceedings of the IEEE BIBM 2020, pp. 2167-2174, 2020. DOI: 10.1109/BIBM49941.2020.9313199