This is work in progress. Expect everything and nothing.
Specific DNA sequences and similar are usually displayed like this (nucleic-acid notation):
GCGGTCATTCACAAATGCTCGCCTTGCTCTCTTATTCTAAGCGTATTTCG
Reading this sucks for the same reason that reading anything in all-caps sucks: There are no ascenders, descenders, or other structure for your eye to orient itself. Several suggestions for different notations have been made, but none of these has taken hold, probably because there is a considerable adaptation effort: People would have to learn completely new symbols before they can start reading.
Acygtus is a font that attempts to address this problem by introducing a vertical structure to regular capital letters:
- A and G have ascenders (and no descenders)
- C, T, and U have descenders (and no ascenders)
- Letters for degenerate bases (B, D, H, K, M, N, R, S, V, W, and Y) have neither ascenders nor descenders.
Since Acygtus is still based on capital letters, there is no adaptation threshold: Everybody can instantly read it. Of course, hope is that some benefits arise from habit.
- Complementary bases (G vs. C and A vs. T/U) differ in having ascenders/descenders.
- C and G are clearly distinguishable beyond vertical offset.
- Monospace enables easy alignment of different sequences.
- Metrics like character width, stem size, and ascender size are almost identical to those of Deja Vu Sans Mono. Thus Acygtus should directly harmonise with that typeface and similar ones (Bitstream Vera).
- Letters for degenerate bases are designed to avoid visual similarities, e.g., V vs. W vs. Y or D vs. B vs. R.
Another approach to this issue is using different colours for the different bases. While this is all nice and proper, colour cannot be used for other illustrative purposes anymore. Of course, if colour is not needed to denote something else, both approaches can be combined.