Homomorphic Computations of Optimal and Approximate Local Alignments

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

Requirement

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