Smith-waterman based Local DNA Alignment with Affine Gap Penalties

Installation

Install using the command below.

library(devtools)
install_github("ruiqi0130/sw_affine")

How to use

Rscript --vanilla hw1.R <input file> <score file>

example

Rscript --vanilla hw1.R input.txt blosum62.txt

Necessary input files

1. inputFile: 2 lines txt file corresponding to two sequences to be aligned.
2. scoreFile: matrix txt file, a amino-acid scoring matrix

Two additional optional inputs may be included for the opening gap and gap extension terms. Defaults for these are: openGap=-2, extGap=-1.

Outputs

1. Two input sequences.
2. Score Matrix used for alignment
3. The best local alignment score
4. The alignment results