4 ms·
It is critical to understand that this article fundamentally misuses the word "homology", which in bioinformatics and molecular evolution is understood to mean
by fastaguy88 3y ago
It is critical to understand that this article fundamentally misuses the word "homology", which in bioinformatics and molecular evolution is understood to mean "sharing a common ancestor". Similarity searches (typically using programs like BLAST, one of the most cited methods in the biomedical literature) look for homologs.
This article is NOT about "homology" detection (which suffix trees are not particularly good for), it is about "identity" detection (which is a related problem, but fundamentally different). It is unfortunate that in the biomedical literature, the word "homology" is often misused in place of "identity" (as in "micro-homology", which is really "micro-identity"), but serious computational biologists try to avoid this misuse of the word "homology".
- Gregaros 3y agoI think rather this is a case of the mathematical notion of [homology](https://en.wikipedia.org/wiki/Homology_(mathematics) https://en.wikipedia.org/wiki/Homology_(mathematics)) - which, roughly, is when a collection of objects combine together to fill a hole (or form the boundary of that hole). In the case of the article, two half-helices ‘overlap’ when they are each two halves of the bounadry of the same DNA segment.
- fastaguy88 3y agoI very much doubt that the widespread misuse of the term "homology" for "identity" by biomedical researchers reflects their deep understanding of mathematical concepts.
- dekhn 3y agoNo, the benchling folks are just wrong. Homology in biology has a long, long history and ignoring that (and mistaking homology and identity). Folks misusing "homology" to mean identity (in the context of making PCR primers, etc) just confused the issue.