Talk:Wikiomics:Repeat finding

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Revision as of 09:42, 1 March 2011 by Darek Kedra (talk | contribs) (repet +)
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RepeatScout possible speedups:

RepeatMasker  input_genome_sequence.fas -lib output_repeats.fas.filtered_1 -norna -nolow -no_is 

-qq (5-10x faster, a bit less sensitive) -pa numbers of parallel processes to use, in case you got multiprocessor or multicore machines

If one is concerned about lower sensitivity of "-qq", then this can be compensated by lowering minimum occurrence threshold (i.e. ("--thresh=5) in the next step.

  • darked 09:26, 23 March 2010 (EDT):


"SeedMasker is public domain software for masking genomes based on over-represented words."

  • darked 15:30, 24 March 2010 (EDT):


GSS sequences including 454 data

Tandem repeat finder parser

@SOURCEFORGE PERL script 2 check