Difference between revisions of "How are the repeats determined?"
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*1) [[http://www.repeatmasker.org RepeatMasker]]<br> | *1) [[http://www.repeatmasker.org RepeatMasker]]<br> | ||
− | There are RepeatMasker libraries available for ''C.elegans ''and''C.briggsae'' are available from the [[http://www.sanger.ac.uk/Projects/C_elegans/REPEATS/ Sanger Institute pages]]. These pages also have some description of the motifs identified.<br> | + | There are RepeatMasker libraries available for ''C.elegans ''and''C.briggsae'' are available from the [[http://www.sanger.ac.uk/Projects/C_elegans/REPEATS/ Sanger Institute pages]]. These pages also have some description of the motifs identified. They can be found in the GFF files thus . . <br> |
+ | |||
+ | <span style="font-family: Courier New;">CHROMOSOME_III RepeatMasker repeat_region 9559 9734 837 . . Target "Motif:PALTA5_CE" 126 307 | ||
+ | </span> | ||
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*2) [[http://tandem.bu.edu/trf/trf.html Tandem Repeat Finder.]] by G. Benson | *2) [[http://tandem.bu.edu/trf/trf.html Tandem Repeat Finder.]] by G. Benson | ||
− | *3) <span style="font-weight: bold;"></span>[[http://www.ncbi.nlm.nih.gov/pubmed/7514951?dopt=Abstract dust]]a low-complexity filter for nucleotide sequences<br> | + | These can be found in the GFF files thus . . |
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+ | <span style="font-family: Courier New;">CHROMOSOME_III tandem tandem_repeat 5079 5117 55 . . Note "3 copies of 14mer"</span> | ||
+ | |||
+ | <span style="font-family: Courier New;"></span> | ||
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+ | *3) <span style="font-weight: bold;"></span>[[http://www.ncbi.nlm.nih.gov/pubmed/7514951?dopt=Abstract dust]]a low-complexity filter for nucleotide sequences (available from WS193)<br> | ||
+ | *4) inv - inverted repeat finding tool by R. Durbin (unpublished) | ||
+ | |||
+ | <span style="font-family: Courier New;">CHROMOSOME_III inverted inverted_repeat 9482 9734 69 . . Note "loop 877, 3 gaps</span>" |
Revision as of 09:19, 17 June 2008
Repeats are determined in several ways.
- 1) [RepeatMasker]
There are RepeatMasker libraries available for C.elegans andC.briggsae are available from the [Sanger Institute pages]. These pages also have some description of the motifs identified. They can be found in the GFF files thus . .
CHROMOSOME_III RepeatMasker repeat_region 9559 9734 837 . . Target "Motif:PALTA5_CE" 126 307
- 2) [Tandem Repeat Finder.] by G. Benson
These can be found in the GFF files thus . .
CHROMOSOME_III tandem tandem_repeat 5079 5117 55 . . Note "3 copies of 14mer"
- 3) [dust]a low-complexity filter for nucleotide sequences (available from WS193)
- 4) inv - inverted repeat finding tool by R. Durbin (unpublished)
CHROMOSOME_III inverted inverted_repeat 9482 9734 69 . . Note "loop 877, 3 gaps"