1. Please go to the following link to find the SSW library:
https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
2. Find the /src/ssw.c for the implementation in C of the Striped Smith Waterman algorithm as your reference.
(https://academic.oup.com/bioinformatics/article/23/2/156/205631)
3. Write a software using a modern C++ SIMD library (e.g., simdpp:
https://github.com/p12tic/libsimdpp) that can perform pairwise alignment with the Striped Smither Waterman algorithm.
a. INPUT: Two sequences (i.e., Seq1 and Seq2) in the FASTA format (https://en.wikipedia.org/wiki/FASTA_format), it is OK to assume no newline in a sequence.
b. OUTPUT: BLAST like output but simplified
Speedup: 0.4X
Seq1: 453 CCAATGCCACAAAACATCTGTCTCTAACTGGTG--TGTGTGT 492
||| ||| |||| |||||| | ||| ||||| |*|||||
Seq2: 17 CCA--GCC-CAAA--ATCTGT-TTTAA-TGGTGGATTTGTGT 51
“|”: match
“ ”: indel, add gaps “-” in the corresponding sequences.
“*” : mismatch
The speedup is calculated against the time needed for the regular banded Smith-Waterman implementeation without SIMD, which means that you need to implemented both versions (i.e., w/ and w/o SIMD).
#include<queue
#include<functional
#include<iostream
Void add()
{
std::cerr<<“1”<<std::endl;
}
struct ADD
{
void operator()()
{
std::cerr<<”2”<<std::endl;
}
};
int main(void)
{
ADD a;
std::queue< std::function<void(void) jobs; jobs.push( std::bind(add) ); jobs.push( std::bind( std::bind(a) ) );
jobs.push( std::bind(a) );
while(!jobs.empty() )
{
jobs.front()(); jobs.pop();
}
return 0;
}
