Detecting microsatellites within genomes: significant variation among algorithms

BMC Bioinformatics

Table 1 Number of detections per megabase, average length (bp), and average divergence (%) of detections for combinations of parameters in the human X chromosome.

TRF alignment weights were set to {2,7,7} when varying the minimum threshold score, and the minimum threshold score to 50 when alignment weights varied. Mreps resolution was 1, 2, 3, and 6. Sputnik mismatch penalty was set to -6 when varying the minimum threshold score, and the minimum threshold score to 7 when varying the mismatch penalty. Match bonus and fail score were always fixed to 1 and -1, respectively. Divergence is deduced from the alignment of the detected sequence with the perfectly repeated corresponding sequence of focal consensus motif:
divergence = (substitutions + insertions + deletions)/alignment length).

ISSN: 1471-2105