[Solved] PL Homework3

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.

1. 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.
2. OUTPUT: BLAST like output but simplified

Speedup: 0.4X

Seq1: 453 CCAATGCCACAAAACATCTGTCTCTAACTGGTGTGTGTGT 492

||| ||| |||| |||||| | ||| ||||| |*|||||

Seq2: 17 CCAGCC-CAAAATCTGT-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;

}