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
• prerequisites
  • Perl
  • Tandem Repeats Finder (trg) (accessed 2010-03-22), last version: 4.04
  • nseg

Simplest run:

• 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 occurring > 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 the filter using i.e. "--thresh=20" (only repeats occurring 20+ times will be kept)

Credits

• Darek Kedra wrote this tutorial