Difference between revisions of "How are the repeats determined?"

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Repeats are determined in several ways.  
 
Repeats are determined in several ways.  
  
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*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]]
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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]].&nbsp; These pages also have some description of the motifs identified.&nbsp; They can be found in the GFF files thus . . <br>
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<span style="font-family: Courier New;">CHROMOSOME_III&nbsp; RepeatMasker&nbsp;&nbsp;&nbsp; repeat_region&nbsp;&nbsp; 9559&nbsp;&nbsp;&nbsp; 9734&nbsp;&nbsp;&nbsp; 837&nbsp;&nbsp;&nbsp;&nbsp; .&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; .&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Target "Motif:PALTA5_CE" 126 307
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</span>
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*2) [[http://tandem.bu.edu/trf/trf.html Tandem Repeat Finder.]] by G. Benson
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These can be found in the GFF files thus . .
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<span style="font-family: Courier New;">CHROMOSOME_III&nbsp; tandem&nbsp; tandem_repeat&nbsp;&nbsp; 5079&nbsp;&nbsp;&nbsp; 5117&nbsp;&nbsp;&nbsp; 55&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; .&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; .&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Note "3 copies of 14mer"</span>
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<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>
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*4) inv&nbsp; - inverted repeat finding tool by R. Durbin (unpublished)
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<span style="font-family: Courier New;">CHROMOSOME_III&nbsp; inverted&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; inverted_repeat 9482&nbsp;&nbsp;&nbsp; 9734&nbsp;&nbsp;&nbsp; 69&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; .&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; .&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Note "loop 877, 3 gaps</span>"
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[[Category:User Guide]]
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[[Category:Curation]]

Latest revision as of 23:32, 13 August 2010

Repeats are determined in several ways.

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


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"