Frith MC, Hamada M, Horton P.

BMC Bioinformatics. 2010 Feb 9;11:80. doi: 10.1186/1471-2105-11-80

Parameters for accurate genome alignment.

Aligned genomes after reversing (not reverse-complementing) them as a negative controls. In these comparisons, all alignments are spurious. A large number of spurious alignments were found, and this could be reduced by masking tandem repeats. Spuriously alignments in tandem repeats get abnormally high scores. “Bad” scoring matrices tend to extend alignments with spurious low-quality arms. The X-drop parameter prevents the aligner from extending alignments too far, but high X-drop values can cause small alignments to be discarded by some software because the score becomes negative.