rvolden / gonk

R2C2/C3POa Smith-Waterman aligner that outputs a list of summed scores

gonk (go for new peaks) is a R2C2 Smith-Waterman aligner that outputs a list of summed scores

Dependencies

• Go

To compile, use make

Usage

gonk takes two sequences, populates a score matrix for the alignment, and sums scores parallel to the main diagonal.

Options:

   -a    First fasta file to align (required)  
   -b    Second fasta file to align (required)  
   -d    Use to exclude the main diagonal (it will be set to zero)  
   -m    Use to output the entire score matrix to stdout  
   -p    Penalty for either gap open or extend (defaults to 25)  
   -o    Output file name (defaults to "SW_PARSE.txt")  

To align and do nothing else:

./gonk -a a.fasta -b b.fasta -p 25

To align and exclude the main diagonal:

./gonk -a a.fasta -b b.fasta -d

To align and output the entire score matrix to matrix.mat:

./gonk -a a.fasta -b b.fasta -m >matrix.mat

Run parameters and a timer are piped to stderr

Affine gap penalty

affine does the same thing as gonk, except uses a linear gap penalty as opposed to a constant penalty. This is more widely used, but is slower and isn't necessary for usage in C3POa. Nevertheless, I have included it here in case it needs to be used down the line. The penalty and outfile options are slightly different:

  -o    Gap open penalty (defaults to 25)  
  -e    Gap extend penalty (defaults to 1)  
  -out  Output file name (defaults to "SW_PARSE.txt")  

affine can be built with make affine

You can install gonk with sudo make install

You can remove gonk and affine executables with make clean

Comparison to old Water aligner