The Problem
In short, my task is to compare two DNA sequences in a way that the general public can recognise the differences. These differences could be slight or major. To represent the differences I can use images, sound and/or animations to help aid.
What's Out There Already
My first task was to find what software is out already. I found no software that claims to demonstrate the differences of DNA sequences. I did find commercial software that produced graphs such as the image below.
To find out how these graphs are created I looked into the process of sequencing DNA. I happened across a video on you tube that described in simple terms the Sanger method.
(https://www.youtube.com/watch?v=iTBTHmhNNbE)
Upon further research I found a paper about DNA representation, which I am currently reading.
(http://www.intechopen.com/books/dna-sequencing-methods-and-applications/dna-repersentation)
Which language
Since working I will be working with files that could be potentially mega bytes in size I decided to test the capabilities of Java and Javascript/HTML5 when reading data from a file. It's my assumption that Javascript/HTML will not be powerful enough to compete the task I intend.
I looked at both methods and the practicality of each, such as speed, librarys available etc.
Audio
Music for the web I found
http://chromium.googlecode.com/svn/trunk/samples/audio/index.html which is a link to a web audio API.
An example I found interesting on here was Drum Machine and a Synth Machine
For Java I found Jsynth which is a library that allows you to generate tones and sound by applying effects.
Images
For javascript I found d3.js. This library allows a programmer to make information more presentable and in a more artistic way. Some I found interesting are
Rounded Rectangles
Steamgraph
Explosions
Rotating arcs
For Java I found Jung. Which I am reading up on.
In short, my task is to compare two DNA sequences in a way that the general public can recognise the differences. These differences could be slight or major. To represent the differences I can use images, sound and/or animations to help aid.
What's Out There Already
My first task was to find what software is out already. I found no software that claims to demonstrate the differences of DNA sequences. I did find commercial software that produced graphs such as the image below.
To find out how these graphs are created I looked into the process of sequencing DNA. I happened across a video on you tube that described in simple terms the Sanger method.
(https://www.youtube.com/watch?v=iTBTHmhNNbE)
Upon further research I found a paper about DNA representation, which I am currently reading.
(http://www.intechopen.com/books/dna-sequencing-methods-and-applications/dna-repersentation)
Which language
Since working I will be working with files that could be potentially mega bytes in size I decided to test the capabilities of Java and Javascript/HTML5 when reading data from a file. It's my assumption that Javascript/HTML will not be powerful enough to compete the task I intend.
I looked at both methods and the practicality of each, such as speed, librarys available etc.
Audio
Music for the web I found
http://chromium.googlecode.com/svn/trunk/samples/audio/index.html which is a link to a web audio API.
An example I found interesting on here was Drum Machine and a Synth Machine
For Java I found Jsynth which is a library that allows you to generate tones and sound by applying effects.
Images
For javascript I found d3.js. This library allows a programmer to make information more presentable and in a more artistic way. Some I found interesting are
Rounded Rectangles
Steamgraph
Explosions
Rotating arcs
For Java I found Jung. Which I am reading up on.