Alignment Viewer is a simple, dependency-free widget to visualize multiple genome sequences.
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sequences = [
'ACTGACTAGCTAGCTAACTG',
'GCATCGTAGCTAGCTACGAT',
'CATCGATCGTACGTACGTAG',
'ATCGATCGATCGTACGATCG'
];
alignmentViewer(sequences).then(function(canvas){
document.body.appendChild(canvas);
});
See the Source Code of the Demo for a slightly fleshier live version. Also, check out the benchmarking test.
alignmentViewer(seqs, config) where:
seqs- an array of sequence stringsconfig- OPTIONAL, an object containing any of the following attributes:config.width- OPTIONAL, the width (in pixels) of each cell. Please note that this is not the width of the output figure. Defaults to 10config.height- OPTIONAL, the height (in pixels) of each cell. Please note that this is not the height of the output figure. Defaults to 10config.showChar- OPTIONAL, should the character be rendered in the cell? Defaults to false. Use with caution, significantly slows down rendering.config.colors- OPTIONAL, an object mapping from the nucleotide to the color of the corresponding cell in the output image. Defaults to the Taylor color scheme:
{
'A' : 'lightgreen',
'G' : 'orange',
'C' : 'yellow',
'T' : 'red',
'ambig': 'white'
}
Fun fact: It's actually alphabet-agnostic, so you can map any character to a color and see it. So you can visualize, say, protein sequences by just setting config.colors to an object mapping from the IUPAC 1-letter codes to the desired color.
Isn't this what MSAViewer is for?
Yup.
MSAViewer is an awesome App. However, it's a difficult widget. What I mean is, it works great on pages where it's the only thing happening. But it has some annoying behaviors. For example, it imports underscore. While this is fine and common, it overwrites window._, which is a huge annoyance when you're using, say lodash.
A big cause of this is the simple fact that MSAViewer does too much. I want a widget that can visualize sequences to judge their alignments at a glance. To accomplish this, I don't need: Fasta importing and exporting (from URLs OR Local files), Consensus Computation, Motif searching, Sorting, filtering, etc. I mean, all of these are cool features, but they should be more available to the programmer than they are to the user. MSAViewer is based on sort-of the opposite principle. It's surprisingly difficult to customize which of these features are made available to the user within MSAViewer. That's how it became a great app, but a terrible widget.
It draws large numbers of enormous sequences blisteringly fast using HTML5's Canvas API. In case you have so many sequences that are so long it begins to get sluggish, it's also promise-based, so you can manage it asynchronously.
Not really, but down the road, I may add some complementary visual elements like sequence logos or gap weights. If you need that stuff, please let me know. Until you do, they're a distant second priority.
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