Table 3

Comparison of the AAGTS and whirl-filtration strategies

Repeat Library

Number of non-redundant input POAP

Fraction of input POAP in graph

Difference in POAP

AAGTS

Whirl-filtration

C. elegans RECON

148,989

0.894

0.972

11,553

Human RpeatScout

378,080

0.981

0.994

4,898

Human RepBase

666,100

0.982

0.979

-2,446

We measure the difference between the procedures by the fraction of aligned positions in the input pairwise alignments that are retained in the multiple alignments produced by each graph procedure. POAP, pairs of aligned positions.

Zhi et al. Genome Biology 2006 7:R7   doi:10.1186/gb-2006-7-1-r7