Wikiomics:Repeat finding

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To simplify, this page assumes eucakariotic genomic DNA repeat finding.

Repeat finding can be divided into two tasks, depending on availability of repeat library:

A) Library exists for a given (or possibly closely related species)

or

B) you construct such library de novo.


Task A is usually a prerequisite step for genome annotation and even blast searches. For newly sequences genomes one should start with B (constructing species specific repeat library).


Detecting known repeats

De novo repeat library construction

For review see: Saha et al. Empirical comparison of ab initio repeat finding programs (2008)

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