How are the repeats determined?
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- 4) inv - inverted repeat finding tool by R. Durbin (unpublished)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"