Abbey

Web-based visualization tool for Sanger DNA sequencing results

Girihlet Inc.

Note: The app I built for this project is not currently available online, but a version of the trace viewer that I created (which was the most challenging part) can be used here:

Drag .ab1 (sequence trace) file(s) here

or,

The Problem

The client found themselves in possession of Sanger DNA sequencing data containing numerous single nucleotide polymorphisms (SNPs). Their data therefore was ill-suited to existing Sanger analysis software solutions, which generally focus on editing the resulting sequence, under the assumption that the sample is homogeneous and does not contain SNPs. We needed a dedicated solution to examine the data and specifically analyze the SNPs.

My Role

As someone with molecular biology training, I took the lead on both designing the core user experience and writing the code. The resulting product allows the user to interactively analyze SNP locations by examining the actual proportion of each nucleotide at a particular position. The resulting data can be exported as a CSV file.

One particular challenge I encountered was achieving smooth animation of the data as the user scrolls back and forth across the sequence. The graph itself is drawn using an interplay of both the canvas element (often used for web-based video games) as well as normal HTML elements, to get both smooth scrolling and interactivity.