zhengqunkoo / smith-waterman

Align sequences of data, with sequential, vectorized, and parallel implementations

Smith-Waterman Algorithm

In the x10 language, for the National University of Singapore's CS3211 module.

Branch Notes

This is the master branch.

Usage

Download x10

• Get the latest version from SourceForge.

Set up Paths

• Add these to your ~/.bashrc.

  export PATH=$PATH:"path/to/x10-2.6.2_linux_x86_64/bin/"
  

Set up Files

git clone https://github.com/zhengqunkoo/smith-waterman
cd smith-waterman

Compile and Run

• To avoid badly formatted stdout, redirect to file.

  x10c++ SmithWaterman.x10 \
  && ./a.out sequences/p53_human.fasta,v sequences/p53_mouse.fasta,v \
  matrices/BLOSUM62,v 5 1 > out \
  && cat out
  

  This command short circuits if there are any compilation errors.
• From Wikipedia's gap example.

  x10c++ SmithWaterman.x10 \
  && ./a.out sequences/wiki_gap1.fasta,v sequences/wiki_gap2.fasta,v \
  matrices/EDNAFULL,v 5 1 > out \
  && cat out
  

• From [Wikipedia's subst example].

  x10c++ SmithWaterman.x10 \
  && ./a.out sequences/wiki_subst1.fasta,v sequences/wiki_subst2.fasta,v \
  matrices/wiki_DNA3,v 0 2 > out \
  && cat out