Should we talk about physical distance in genetics as number of base pairs (kbp, Mbp, and so on) or bases (kb, Mb)?

I got into a discussion about this recently, and I said I’d continue the struggle on my blog. Here it is. Let me first say that I don’t think this matters at all, and if you make a big deal out of this (or whether ”data” can be singular, or any of those inconsequential matters of taste we argue about for amusement), you shouldn’t. See this blog post as an exorcism, helping me not to trouble my colleagues with my issues.

What I’m objecting to is mostly the inconsistency of talking about long stretches of nucleotides as ”kilobase” and ”megabase” but talking about short stretches as ”base pairs”. I don’t think it’s very common to call a 100 nucleotide stretch ”a 100 b sequence”; I would expect ”100 bp”. For example, if we look at Ensembl, they might describe a large region as 1 Mb, but if you zoom in a lot, they give length in bp. My impression is that this is a common practice. However, if you consistently use ”bases” and ”megabase”, more power to you.

Unless you’re writing a very specific kind of bioinformatics paper, the risk of confusion with the computer storage unit isn’t a problem. But there are some biological arguments.

A biological argument for ”base”, might be that we care about the identity of the base, not the base pairing. We note only one nucleotide down when we write a nucleic acid sequence. The base pair is a different thing: that base bound to the one on the other strand that it’s paired with, or, if the DNA or RNA is single-stranded, it’s not even paired at all.

Conversely, a biochemical argument for ”base pair” might be that in a double-stranded molecule, the base pair is the relevant informational unit. We may only write one base in our nucleotide sequence for convenience, but because of the rules of base pairing, we know the complementing pair. In this case, maybe we should use ”base” for single-stranded molecules.

If we consult two more or less trustworthy sources, The Encylopedia of Life Sciences and Wiktionary, they both seem to take this view.

eLS says:

A megabase pair, abbreviated Mbp, is a unit of length of nucleic acids, equal to one million base pairs. The term ‘megabase’ (or Mb) is commonly used inter-changeably, although strictly this would refer to a single-stranded nucleic acid.

Wiktionary says:

A length of nucleic acid containing one million nucleotides (bases if single-stranded, base pairs if double-stranded)

Please return next week for the correct pronunciation of ”loci”.

Literature

Dear, P.H. (2006). Megabase Pair (Mbp). eLS.