Talk:Wikiomics:Repeat finding: Difference between revisions
Darek Kedra (talk | contribs) (RepeatMasker for RepeatScout speedup) |
Darek Kedra (talk | contribs) (→TANTAN: new section) |
||
| (6 intermediate revisions by the same user not shown) | |||
| Line 10: | Line 10: | ||
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. | 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. | ||
*'''[[User:Darek Kedra|darked]] 09:26, 23 March 2010 (EDT)''': | *'''[[User:Darek Kedra|darked]] 09:26, 23 March 2010 (EDT)''': | ||
== Seedmasker == | |||
"SeedMasker is public domain software for masking genomes based on over-represented words." | |||
http://www.drive5.com/seedmasker/ | |||
*'''[[User:Darek Kedra|darked]] 15:30, 24 March 2010 (EDT)''': | |||
== ReRep == | |||
GSS sequences including 454 data | |||
http://www.biomedcentral.com/1471-2105/9/366/ | |||
http://bioinfo.pdtis.fiocruz.br/ReRep/ | |||
== Tandem repeat finder parser == | |||
@SOURCEFORGE PERL script 2 check | |||
http://sourceforge.net/projects/trfparser/ | |||
== REPET == | |||
http://urgi.versailles.inra.fr/index.php//Tools/REPET | |||
== TANTAN == | |||
new algorithm from 2011: | |||
www: http://www.cbrc.jp/tantan/ | |||
article: http://nar.oxfordjournals.org/content/39/4/e23.full | |||
Revision as of 11:20, 11 March 2011
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
"SeedMasker is public domain software for masking genomes based on over-represented words." http://www.drive5.com/seedmasker/
- darked 15:30, 24 March 2010 (EDT):
ReRep
GSS sequences including 454 data
http://www.biomedcentral.com/1471-2105/9/366/
http://bioinfo.pdtis.fiocruz.br/ReRep/
Tandem repeat finder parser
@SOURCEFORGE PERL script 2 check http://sourceforge.net/projects/trfparser/
REPET
http://urgi.versailles.inra.fr/index.php//Tools/REPET
TANTAN
new algorithm from 2011:
www: http://www.cbrc.jp/tantan/
article: http://nar.oxfordjournals.org/content/39/4/e23.full
