Local-Alignment

Introduction

A Go implementation of the Smith–Waterman algorithm. This program will find an optimal local alignment for two DNA, RNA or amino acid sequences.

Installation

Install Go

Clone the repository

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

Build localalign.go

$ cd Local-Alignment; go build localalign.go

Usage

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

$ ./localalign -seq1=examples/seq1 -seq2=examples/seq2

Options

• -seq1
  • The location of a text file containing the first sequence to align
• -seq2
  • The location of a text file containing the second sequence to align
• -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 2. 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 -2. This is only used when a similarity matrix is not specified.
• -gapopen
  • The score that is assigned to a nucleotide or amino acid that is aligned to a gap opening. This value defaults to -1.
• -gapextend
  • The score that is assigned to a nucleotide or amino acid that is aligned to a gap extension. This value defaults to the same value is gapopen.