Alignment Plots Package

Overview

Alignment plots visualize the relationship between nucleotide or amino acid sequences.

Example

The following example demonstrates how to print an alignment plot of two sequences to stdout.

package main

import (
	"fmt"
	"log"

	"github.com/DanielSchuette/bioinformatics/alignmentplots"
)

func main() {
	// create an `Alignment' struct
	align := &alignmentplots.Alignment{
		SeqA: "MEEPQSDPSVEPPLSQET",   /* human TP53 AA 1-18 */
		SeqB: "EPQSDPSVEPPLSQETFSDL", /* human TP53 AA 3-22 */
	}

	// plot the resulting struct
	fmt.Println(align)

	// align the two input sequences `SeqA' and `SeqB'
	align.Align()

	// plot the alignment
	err := align.Plot("My First Alignment Plot")
	if err != nil {
		log.Fatalf("error while plotting: %v\n", err)
	}
}

This program generates the following output:

Matching residues are represented by certain characters (0 for matches that lie within the main diagonal or have at least one diagonal neighbor and x for matches that are not associated with a sequence of at least two diagonal matches) and are color-coded.

License

The code in this repository is MIT licensed.