into the roots

Sunday, July 26, 2026

Saturday, March 21, 2026

Column chromatography

A jar of snacks (namkeens) demonstrate the principles of column chromatography to a fairly accurate extent.

In a column consisting of differently sized particles, gravity arranges them over time to a particular configuration

The smallest fragments gravitate to the bottom, followed by medium ones, until a gradient is formed from largest to smallest particles, to to bottom of the jar

Sunday, October 20, 2024

Next generation sequencing: Part 1

Imagine solving a puzzle with 100 pieces, each piece a centimeter in size, something like this:

The genome is considerably larger than this puzzle and has much more than 100 pieces to assemble, in a typical NGS run

A few things are immediately obvious

1. The size of each piece (a 'read' in NGS terminology) matters; larger pieces make solving the puzzle exponentially easier

2. A few pieces seem to fit in multiple places of the puzzle; they are similar to a great degree, (like the pieces containing black hair in this puzzle), however, differ ever so slightly (maybe in only a few pixels, or in NGS terms, nucleotides)

3. Some pieces are repetetive (like the 'blue sky' in this puzzle), which add to the difficulty of assembling the puzzle; they are equivalent to the nucleotide repeat sequences encountered in reads of NGS

4. In this puzzle, no two pieces overlap. However, NGS reads will often overlap with each other.

Together, these are the core issues in the genome assembly problem, i.e. reconstructing a genome from its fragments when you have no 'reference genome' to look up to.