next up previous
Next: -r, Min match length Up: Parameters Previous: -g, Extension max gap,

-p, Length of exact match pairs, (positive integer)

Running time of LTR_FINDER is very sensitive to this parameter. The program only selects pairs that are longer than this value to do further processes from all exact match pairs detected. If a very small value is given, LTR_FINDER will spend much time on randomly matched short sequences. We use P-value to estimate proper value of -p, that is, the probability of exact match of length longer than $L$ occurs if 2 sequences are drown randomly. In Waterman 1989(, ), under independent letter model, using asymptotic extreme value distribution, P-value were worked out analytically. Now if one assign the P-value, length can be deduced. From experiments, 20 is appropriate in most situation, and we suggest not using of value less than 15.