Getting started

git clone https://github.com/wxiaoning/longest-common-subsequence.git
cd longest-common-subsequence;
if you're on the KNC platforms
	then use the following make command:
	make ARCH=LCS_KNC
else if you're on the KNL platforms
	then use the following make command:
	make ARCH=LCS_KNL
./main

Introduction

Longest-Common-Subsequence(LCS) is a software package for accelrating bit-parallel longest common subsequence algorithm on Xeon Phi clusters, including KNC clusters and KNL clusters. The database used in the experiments are synthetic, you can use the file input.c and input_ref.c to generate synthetic subject and query data independently. You need to create a new folder named database firstly. The subject and query files are stored in database folder. The subject file is named seq.fasta and the query file is named input_seq[number].fasta. If you're running on the cluster, there're as many query files as MIC cards named input_seq0.fasta, input_seq1.fasta, input_seq2.fasta and so on. The results are stored in result[number].fasta. It gives the length of longest common subsequence of two sequences.

Availability

The latest source code of LCS is freely available st github. After you acquire the source code, use the front make instructions to compile and copy the single executable main to the destination you want.

Questions

If you have questions about LCS, you may send the questions to [email protected].