| Type: | Package |
| Title: | Sequence Alignment and Visualization Tool |
| Version: | 0.1.1 |
| Description: | Computes the optimal alignment of two character sequences. Visualizes the result of the alignment in a matrix plot. Needleman, Saul B.; Wunsch, Christian D. (1970) "A general method applicable to the search for similarities in the amino acid sequence of two proteins" <doi:10.1016/0022-2836(70)90057-4>. |
| Imports: | plot.matrix, graphics |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.1 |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2024-02-06 10:16:42 UTC; Leonn |
| Author: | Leonard Persson Norblad
 [aut, cre],
Kamil Slowikowski
[ctb] |
| Maintainer: | Leonard Persson Norblad <leonard.norblad@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-02-07 17:50:13 UTC |
Sequence Alignment Tool
Description
Sequence alignment and visualization tool designed to enhance understanding of sequence alignment algorithms, such as the Needleman-Wunsch algorithm. Through detailed matrix plot visualizations with arrows illustrating the path of different alignments, users can gain insights into how these algorithms score and identify optimal alignments between two sequences.
Getting started
Install the SeqAlignR package from CRAN using:
install.packages("SeqAlignR")Load the SeqAlignR package into your R session:
library(SeqAlignR)
Explore the documentation for
align_sequencesor see the example below:?align_sequences
Author(s)
Leonard Persson Norblad leonard.norblad@gmail.com (ORCID)
References
The graphics in the package were inspired by this code by Kamil Slowikowski (ORCID).
Examples
seq1 <- "GCATGCG"
seq2 <- "GATTACA"
# Run the Needleman-Wunsch algorithm
alignment1 <- align_sequences(seq1, seq2, d = -1, mismatch = -1, match = 1, method="needleman")
# Print the alignments
print(alignment1)
# Plot the matrix
plot(alignment1)
Sequence Alignment
Description
Performs sequence alignment on two sequences by a user specified alignment method. As of now, only the Needleman-Wunsch algorithm is supported.
Usage
align_sequences(seq1, seq2, d, mismatch, match, method = "needleman")
Arguments
seq1 |
First sequence to align. |
seq2 |
Second sequence to align. |
d |
Gap penalty, should be negative. |
mismatch |
Mismatch penalty, should be negative. |
match |
Match score, should be positive. |
method |
Name of alignment algorithm. Currently only supports "needleman". |
Value
Object of class alignment representing the alignment result.
This object can be utilized with the plot.alignment function to visualize
the alignment matrix and the print.alignment function to display alignments
in the console.
References
For more details on the Needleman-Wunsch algorithm, see the wikipedia page.
Examples
seq1 <- "GCATGCG"
seq2 <- "GATTACA"
# Run the Needleman-Wunsch algorithm
align_sequences(seq1, seq2, d = -1, mismatch = -1, match = 1)
Plot Alignment Matrix
Description
Produces a plot displaying the alignment matrix of seq1 and seq2.
Usage
## S3 method for class 'alignment'
plot(x, ...)
Arguments
x |
Object of class |
... |
Additional parameters to be passed to the |
Details
The first sequence (seq1) is represented by the columns and the second sequence (seq2) is represented
by the rows. The first column and first row are left bank, meaning a gap. Each cell in the matrix displays the score.
The subtitle states the match, mismatch and gap penalty d used in the algorithm.
A mismatch is shown by the red arrows, a match by the blue arrows, and a gap by the green arrows.
The alignment(s) with the highest score are highlighted with thick gray borders.
Value
Plot of the alignment matrix.
References
The implementation is inspired by the visualization (code) by Kamil Slowikowski (ORCID).
Examples
seq1 <- "GCATGCG"
seq2 <- "GATTACA"
# Run the Needleman-Wunsch algorithm
alignment1 <- align_sequences(seq1, seq2, d = -1, mismatch = -1, match = 1)
# Plot the matrix
plot(alignment1)
Print Alignments
Description
Prints the alignments between seq1 and seq2 with the highest score.
Usage
## S3 method for class 'alignment'
print(x, ...)
Arguments
x |
Object of class |
... |
Additional parameters to be passed to the |
Details
The printed message includes the alignment score. This function may display multiple alignments, as alignments with the same score are possible.
Value
Console print of alignments.
Examples
seq1 <- "GCATGCG"
seq2 <- "GATTACA"
# Run the Needleman-Wunsch algorithm
alignment1 <- align_sequences(seq1, seq2, d = -1, mismatch = -1, match = 1)
# Print the alignments
print(alignment1)