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
- 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 
- command line
You have to have a FastA file (it can be multiple FastA). Type:
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)
command line only, requires compilation
current version (2010-03): 1.05
- PPT presentation presenting algorithm: http://bix.ucsd.edu/repeatscout/repeatscout-ismb.ppt
- publication (PDF)De novo identification of repeat families in large genomes 2005
- build frequency table
build_lmer_table -sequence input_genome_sequence.fas -freq output_lmer.frequency
output_lmer.frequency file can be still quite large (1.7Gb for 900Mb fasta file)
- create fasta file containing all kinds of repeats
RepeatScout -sequence input_genome_sequence.fas -output output_repeats.fas -freq output_lmer.frequency
RAM usage (RepeatScout): > 17Gb for 800Mb genomic sequence.
The output (output_repeats.fas) is a fasta file with headers (>R=1, >R=232 etc.). It contains also trivial simple repeats (CACACA...), tandem repeats
- filter out short (<50bp) sequences. Remove "anything that is over 50% low-complexity vis a vis TRF or NSEG.". Perl script.
It does require trg and nseg to be on the PATH, or setting env variables TRF_COMMAND and NSEG_COMMAND pointing to their location
filter-stage-1.prl output_repeats.fas > output_repeats.fas.filtered
- run RepeatMasker on your genome of interest using filtered RepeatScout library
RepeatMasker input_genome_sequence.fas -lib output_repeats.fas.filtered
Output used for the next step: input_genome_sequence.fas.out
- filtering putative repeats by copy number. By default only sequences occuring > 10 times in the genome are kept
cat repeats.lib | filter-stage-2.prl --cat= input_genome_sequence.fas.out filter-stage-2.prl
You can modify tthe filter using i.e. "--thresh=20" (only repeats occuring 20+ times will be kept)