alignmentplots

README

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.

Documentation

Overview

Package alignmentplots ...

Index

• Constants
• type Alignment
  • func (a *Alignment) Align()
  • func (a *Alignment) Plot(title string) error
  • func (a *Alignment) String() string

Constants

const (
	// returns the current version of `alignmentplots'
	Version = "0.0.1"
)

Package-level constants that determine certain behaviors of e.g. the plotting functionality.

Types

type Alignment

type Alignment struct {
	// sequence A will be plotted in rows
	SeqA string

	// sequence B will be plotted in columns
	SeqB string

	// the alignment matrix indicates sequence similarities
	AlignmentMatrix [][]bool
}

Alignment holds two protein sequences and optionally their alignment matrix.

func (*Alignment) Align

func (a *Alignment) Align()

Align populates the `AlignmentMatrix' field of an `Alignment' struct. It must be called before an alignment plot can be created.

func (*Alignment) Plot

func (a *Alignment) Plot(title string) error

Plot creates a dot plot that visualizes the alignment of two protein sequences.

func (*Alignment) String

func (a *Alignment) String() string

String ensures that `Alignment' implements the `Stringer' interface for pretty printing.