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Smith-Waterman

Descriptions:

This package implements a Smith-Waterman local alignment algorithm. The default gap penalties are: opening gap -2, extension gap = -1.

Input:

  1. A txt file containing two FASTA format sequences
  2. A txt file containing blosum62 similarity scoring matrix

Ouput:

  1. A txt file containing the input sequences, score matrix, and best local alignment results.

Installation:

pip install "git+https://github.com/annasu1225/Smith-Waterman.git"

Usage:

python SW.py -i inputfile -s scorefile

Example:

python SW.py -i input.txt -s blosum62.txt

Contact:

[email protected]

References:

  1. CMU CMSC423 Gap Penalties Lecture Slides
  2. Smith-Waterman Algorithm by Slavianap