Friday, August 03, 2012

Imagine: A Faster Nanopore DNA Sequencing Technique

Via this paper, I was reminded of a now famous quote by David Brady widely seen as a reasoning for compressive sensing  “if it is possible to compress measured data, one might argue that too many measurements were taken”.[1].

In DNA sequencing, some folks are considering compressive BLAST but this is really an after the fact technique, What about compressing the data during acquisition ? Let's say that since a lot many parts of DNA is non coding, or that DNA has some prior known sequence, can we argue that current DNA sequencing hardware and techniques are taking too many measurements ? In that case, how can compressive sensing help in that regard ? Can it improve the speed for reading DNA or can it improve the accuracy at which sequencing takes place.

Take for instance the latest and most promising technique, the Nanopore DNA sequencing (figure from Oxford Nanopores Technologies) technology which basically acts as a mesh screen and recognize a specific nucleotide (G, A, T,C) by how different the voltage across the pore varies. . 

If the pore were to be bigger, the voltage measurement would be a combination of several nucleotides which could easily be put as a compressive sensing problematic.

[1]  David Brady,  Optical Imaging and Spectroscopy 

No comments: