Doubt about the process of annotation, detection, identification and classification of transposable elements

Question

[MarcosCosta]

I'm new to bioinformatics, transitioning from the field of computing. I've been tasked with assisting in the development of a pipeline for transposable element annotation. As part of my preparation, I've been exploring articles on the topic. However, I've encountered various terms such as "TE detection", "TE identification", and "TE classification". My question is: do these terms denote distinct processes, or are they all integral to the TE annotation process? Appreciate any insights on this matter."

Answer 1

[Mensur Dlakic]

Depends on the context. TE detection and TE identification could mean the same thing if they refer to presence/absence of TEs. TE identification could also mean the assignment of TEs to a particular class, in which case it would be synonymous with TE classification.

For practical purposes all 3 terms probably mean the same thing, because it would be unlikely that there is a method that only detects TEs without simultaneously classifying them into a particular group.

[MarcosCosta]

Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?