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

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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>"
 
<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  • 4) inv  - inverted repeat finding tool by R. Durbin (unpublished)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"