Global-Alignment

Introduction

A python implementation of the Needleman–Wunsch algorithm. This program will find the optimal global alignments for two DNA, RNA or amino acid sequences.

How to get the code

Type the following command into the terminal

$ git clone https://github.com/Brandonag1997/Global-Alignment.git

Usage

The global alignment program takes 2 texts files containing either nucleotide or amino-acid sequences. To run navigate to ./Global-Alignment and make globalalign.py executable by running

$ chmod +x globalalign.py

The program takes at least 2 arguments, the locations of the sequences you want to align. For example

$ ./globalalign.py ./examples/exampleSequence1.txt ./examples/exampleSequence2.txt

This will output the best alignments for the 2 sequences and save the results to Output.txt

Options

• --similarity_matrix
  • This optional parameter specifies the similarity matrix if no matrix is specied a simple match/mismatch/gap scoring matrix will be used
  • Available similarity matrices include
    • BLOSUM62
    • BLOSUM30 increased by 5 up to BLOSUM90
    • BLUSOM100
    • PAM10 increased by 10 up to PAM500
    • NUC.4.2 and NUC.4.4
    • DAYHOFF
    • GONNET
    • IDENTITY
    • MATCH (gives the same results as the default)
• --match
  • The score that is assigned to 2 nucleotides or amino acids that match. This value defaults to 1. This is only used when a similarity matrix is not specified.
• --mismatch
  • The score that is assigned to 2 nucleotides or amino acids that do not match. This value defaults to -1. This is only used when a similarity matrix is not specified.
• --gap
  • The score that is assigned to a nucleotide or amino acid that is aligned to a gap. This value defaults to -1.