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alignment's Introduction

Alignment

Protein sequences alignment using the Smith-Waterman algorithm with an affine gap penalty.

Getting Started

Here is an example of how to install the package and use it.

Installtion

pip install git+https://github.com/yzJiang9/alignment.git

Usage

from alignment import smith_waterman

inputFile = 'path/To/Input'
scoreFile = 'path/To/ScoreFile'
outputFile = 'path/To/Output'

smith_waterman.runSW(inputFile, scoreFile, outputFile, openGap = -2, extGap = -1)

blosum62.txt is provided and used as a substitution matrix in demos. Demos can be found under examples.

An output file consists of three parts as follows.

  • Sequences: two sequences in the input file. The input file should only contain two sequences, each line for one.
  • Scoring matrix: matrix calculated by the Smith-Waterman algorithm (by default, gap opening penealty is -2 and gap extension penalty is -1).

Smith-Waterman Algorithm

  • Best local alignments: two sequences with aligned results: | for a match and - for a gap.

License

Distributed under the GPLv3 License. See LICENSE for more information.

Contact

Yunzhe Jiang - [email protected].

Course - CB&B752: Biomedical Data Science: Mining and Modeling given by Prof. Mark Gerstein at Yale Univerisity.

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