SmithWaterman

1. Aim of the project

The project has been developed as part of the exam for the Scientific Programming course (A.A. 2021-2022) of the Bioinformatics for Computational Genomics Master's Degree.
The aim of the project was to develop a package in R which implements the local pairwise alignment method using the Smith-Waterman (S-W) algorithm to find the optimal global alignment between two sequences.
This project has been developed as a standard R package that could be used locally on RStudio, not as a compliant Bioconductor package.

The main expected outcomes of the package were the following:

appropriate data structures for the implementation of the S-W algorithm;
a function that takes as parameters:
a1. cost of a match,
a2. cost of a mismatch,
a3. cost of a gap,
b. first nucleotide sequence,
c. second nucleotide sequence.
As result, the function returns on optimal alignment between the two input sequences;
documentation of the design and development;
the implementation should work smoothly for sequences of length equals to ~500 nucleotides;
an optional unit testing implementation.

2. What does the repository store?

One possible tool that is used in R to develop packages is devtools, which allows the instant creation of a "skeleton" that provides the basic structure for organizing the package in a series of files and directories.
The content of this repository reflects the basic files and directories necessary to build a complete package, which are:

DESCRIPTION file: it describes the project, sets up what packages are suggested for the development tasks and applies a license.
NAMESPACE file: it is automatically generated and it lists the function in the package.
R directory: it stores the .R code of the main function.
man directory: it contains the documentation that will become the help page in the package.
tests directory: it stores the files for unit testing of the function, relying on the testthat package.
vignettes directory: inside it is stored a very thorough description of the package developmental process in form of a .Rmd file, with explanation of the code abd a usage example. The RMarkdown file can be converted into an HTML file with knitr.

There are also other files referred to the package inside the repository which are automatically generated, plus some .gitignore files that refer to the version control changes.

The package has been developed with the following system specifics:

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

3. Package installation

The package can be installed from Github with devtools in RStudio with the following commands:

> if (!require("devtools")) {install.packages("devtools")}

> devtools::install_github("sonechkina/SmithWaterman")

Once the package is installed, it can be loaded in the current RStudio session:

> library(SmithWaterman)

The help page for the function of the package can be browsed in RStudio session with the following command:

> ?smith_waterman