Bits per Base

A commenter mentioned that they heard nucleotide bases took 7 bits to store.

7 bits is the encoding for ASCII characters, which are used to store literal “A T C G”s in a text editor. There are 4 bases, so one only need 2 bits (2² = 4 bases). These bases could be numbered like this:

00 = A
01 = G
10 = C
11 = T

This encoding further has the convenient property that the bits can be inverted to get the complementary DNA strand. Storing bases as ASCII is OK for small, human readable files, but otherwise, it’s a gross waste of storage, bandwidth, and processor resources (about a 350% waste). This “data inflation” could be much worse if the files are encoded using unicode or other bigger character sets most used in foreign countries.

Abbreviations

Josh, my science editor, will disagree about this because “biologists don’t use the Internet” and “base 2 is for nerds,” but PLEASE, define all acronyms and unit abbreviations in a glossary! I was reviewing “A Short Guide to the Human Genome” by Cold Spring Harbor Lab Press, and in a table of chromosome sizes, the data is measured as Mb (with no explanation).

What is “Mb?”

DATA: “Mb” is “megabits,” which is 2²⁰ bits. Each base is two bits, so 2¹⁹ = 524288 bases per unit “Mb.”

BIOLOGY: “Mb” is “megabases,” which is 1,000,000 bases per unit “Mb.”

Either interpretation is valid, and this is a serious problem as biology and computer science continue to collaborate. If NASA and Lockheed Martin can bungle units at the cost of a $327MM Mars Climate Orbiter extraterrestrial nose dive, you can certainly bungle a genomic experiment due to confused units, too.

There’s a joke that biologist’s don’t have new math, so they invent vocabulary to keep others out of their field. Please do not led credence to this joke.

I don’t say that “biologists don’t use the internet”, but it’s generally not an issue to know whether you’re using megabytes or megabases; the context tells you. If you’re dealing with DNA, it just doesn’t make sense to measure it in computational units of storage (ie megabytes), because this is effectively meaningless. If a segment of DNA is, say, 5Mb, the sentence doesn’t really make sense if you had a 5 megabyte fragment of DNA.

I suppose some people may get confused, but I think generally it’s a non-issue. In that particular book, if it’s targeted to people familiar with the field, they will know what Mb stands for. However, if it’s an introductory book, some explanation probably should be given.

The quote my from gchat logs is:

Josh: I disagree, but whatever. CS corrupted the metric system with base 2

Josh:

It took a global corps of scientists approximately $500 million and 13 years to identify the more than 35,000 genes of the human genome. Five years later, Boston College Biologist Gabor Marth and his research team have developed software that can analyze half a million DNA sequences in 10 minutes.The Marth laboratory’s proprietary PyroBayes software is one of a new breed of computer programs able to accurately process the mountains of genome data flowing from the latest generation of gene decoding machines, which have placed a premium on computational speed and accuracy in data-crunching fields known as bioinformatics and high-throughput biology, said Marth, an associate professor of Biology.

“We’re on the edge of a real technological revolution that I think will help us understand the genetic causes of diseases in humans and how genetic materials determine traits in animals,” said Marth. “It is going to lead to less expensive technologies that will allow researchers to decode any individual.” … Continue Reading »