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).

Detecting known repeats

Most comonly used: Repeatmasker

RepeatMasker

• web site: http://www.repeatmasker.org/
• current version (checked on 2010-03.22): 3.2.8
• documentation: http://www.repeatmasker.org/webrepeatmaskerhelp.html

• 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 programs recommendations based on test see: Saha et al. Empirical comparison of ab initio repeat finding programs (2008)

For an extensive review listing tens of programs: Lerat E.Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs (Nov 2009)

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

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