Figure 3

Markov clustering of D. melanogaster BEL/Pao elements. We clustered all 178 BEL/Pao elements from D. melanogaster into ten families based on their sequence similarity using the MCL algorithm [27] from within BioLayout [46]. We refer to these families as MCL families. A node in the graph represents one element. Edges represent nucleotide sequence similarity between two elements (see Methods for details). Elements clustered into the same family are shown in the same color. The absence of an edge between two elements, indicates that the elements do not share sufficiently high sequence similarity over at least 500 bp (see Methods). We compared the elements of the MCL families to previous annotation of these elements in the D. melanogaster genome and in Repbase Update. Each MCL family is labeled with two names separated by a slash. The left name is from the Drosophila genome annotation, the right name is from Repbase Update. Dashes '-' indicate that a family has not been previously annotated. Note that one family has two names: 3S18 in the genome annotation and BEL in Repbase Update. Elements from family d) were previously annotated as belonging to two different families.