Wikiomics:Repeat finding: Difference between revisions
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=De novo repeat library construction= | =De novo repeat library construction= | ||
For | For programs recommendations based on test see: Saha et al. [http://nar.oxfordjournals.org/cgi/content/full/gkn064v1 Empirical comparison of ab initio repeat finding programs] (2008) | ||
For an extensive review listing tens of programs: Lerat E.[http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy2009165a.html Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs ] (Nov 2009) | |||
==RepeatScout== | ==RepeatScout== |
Revision as of 09:29, 22 March 2010
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.