Efficiently storing and analyzing these sequences is a critical challenge. Furthermore, the ability to analyze large sequences of data are increasingly critical. In this post, we will explore a method to compress DNA using 4-bits per nucleotide in pure Rust, that allows us to generate Complementary base pairs in its compressed form.

This technique is especially useful in DNA analytical pipelines, where performance and memory constraints are critical. By minimizing the footprint of each sequence, we simultaneously reduce storage overhead and in-memory costs, without sacrificing speed or the ability to operate directly on compressed data.

Background ​

DNA Bases and IUPAC Codes ​

There are 15 IUPAC codes. The ones that most are familiar with are "A", "G", "C", and "T", representing the four standard DNA bases. However, DNA sequencing often produces ambiguous results. The remaining 11 codes are for these cases. For example, "R" can represent "G" or "A", while "N" can represent any nucleotide.