There is a large amount of variation in the percentage of repeats classified by one method and multiple methods as compared to those of C. elegans. This also demonstrates that one particular method will not be sufficient for classification and that the combination of several methods is required.
4.2 Classification of C. Elegans repeats identified de novo with RepeatScout The next step was to compare the repeats identified de novo with RepeatScout and those existing in Repbase. This provides an estimation of the performance of RepeatScout and REPCLASS combined. 35.8% (145 repeats) of the RepeatScout output was classified by REPCLASS. Unclassified Repbase Classified by REPCLASS
263
102
22
43
Figure 4.3: Classification distribution for C. elegans repeats identified de novo using RepeatScout
408 repeat consensuses were identified and 102 repeats match those of Repbase. RepeatScout identified 38 repeats with proper ends matching with repeats in Repbase. 22 repeats that are part of Repbase were not identified by the de novo method. 43 of the 54