Wikiomics:Repeat finding

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Revision as of 08:26, 22 March 2010 by Darek Kedra (talk | contribs) (RepeatScout)
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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)


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

Most comonly used: Repeatmasker


  • Online web server [1]
  • command line

You have to have a FastA file (it can be multiple FastA). Type:

repmask your_sequence_in_fasta_format

You will get a file: your_sequence_in_fasta_format.masked --- name tells all

species options (choose only one):

-m(us) masks rodent specific and mammalian wide repeats
-rod(ent) same as -mus
-mam(mal) masks repeats found in non-primate, non-rodent mammals
-ar(abidopsis) masks repeats found in Arabidopsis
-dr(osophila) masks repeats found in Drosophilas
-el(egans) masks repeats found in C. elegans

De novo repeat library construction

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


command line only, requires compilation


current version (2010-03): 1.05


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

RAM usage: > 17Gb for 800Mb genomic sequence.