XSW

• A fast Smith-Waterman Algorithm Implementation on Intel Xeon Phi Coprocessors.

Introduction

• XSW is a fast implementation of Smith-Waterman algorithm performed on the Intel(R) MIC platform. We achieved a speed of 70G CUPS (cell update per second) on a single Xeon Phi 7110p in native mode and 100G CUPS on a E5-2620 CPU with one Xeon Phi 7110p in offload mode.

##Installation and Usage

• Three files must be provided to run XSW: the scoring matrix, query sequence and the database. The query sequence and database should be in FASTA format. For example, steps to run the query testRefSeq0511.txt to the database db.env_nr with the default gap penalties and scoring matrix are as following:

** For native version: **

• Step 1: Preproccess the database:

  ./makemicdb.out db.env_nr 244

  [NOTE:] if your Xeon Phi has 61 cores, it is 244, if 60 cores it is 240.

• Step 2: Upload the database and program to xeon phi:

  scp db.env_nr*.* blosum62.mat testRef* XSW mic0:

• Step 3: Login xeon phi card:

  ssh mic0

• Step 4: Run XSW on xeon phi:

  ./XSW blosum62.mat testRefSeq0511.txt db.env_nr

** For offload version: **

• Step 1: Preproccess the database:

  ./makemicdb4.1.out db.env_nr

• Step 2: Run XSW:

  ./XSW blosum62.mat testRefSeq1023.txt db.env_nr

##Reference

• ** Paper is under submission.**

##Authors and Contributors

• Weiguo Liu is the corresponding author.

##Support or Contact

• If you have any questions, please contact: Weiguo,Liu ( weiguo.liu@sdu.edu.cn).