Wikiomics:Repeat finding

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).

De novo repeat library construction

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

RepeatScout

command line only, requires compilation

Site: http://bix.ucsd.edu/repeatscout/

current version (2010-03): 1.05

Documentation:

• http://bix.ucsd.edu/repeatscout/readme.1.0.5.txt
• PPT presentation presenting algorithm: http://bix.ucsd.edu/repeatscout/repeatscout-ismb.ppt
• publication (PDF)De novo identification of repeat families in large genomes 2005

Simplest run:

build_lmer_table -sequence input_sequence.fas -freq output_lmer.frequency
RepeatScout -sequence input_sequence.fas -output output_repeats -freq  output_lmer.frequency