Sequence Comparison.pdf

6.6 Generalizations of Spaced Seeds 113
Table 6.4 Top-ranked spaced seeds for different similarity levels and weights. The sign ‘−’ means
that the corresponding seed is not among the top 10 seeds for the similarity level and weight. This
is reproduced from the paper [48] of Choi, Zeng, and Zhang; reprinted with permission of Oxford
University Press.
W
Good spaced seeds
Rank under
a similarity level (%)
65 70 75 80 85 90
9 11*11*1*1***111
11*1*11***1*111
11*11**1*1**111
10 11*11***11*1*111
111**1*1**11*111
11*11**1*1*1**111
11 111*1**1*1**11*111
111**1*11**1*1*111
11*1*1*11**1**1111
12 111*1*11*1**11*111
111*1**11*1*11*111
111**1*1*1**11*1111
13 111*1*11**11**1*1111
111*1**11*1**111*111
111*11*11**1*1*1111
14 111*111**1*11**1*1111
1111*1**11**11*1*1111
1111*1*1*11**11*1111
15 1111**1*1*1*11**11*1111
111*111**1*11**1*11111
111*111*1*11*1**11111
1111*11**11*1*1*11*1111
16
1111**11*1*1*11**11*1111
1111*1**11*1*1**111*1111
111*111*1**111*11*1111
1 1 1 1 1 1
2 2 2 2 2 3
4 4 4 4 4 4
1 1 1 1 1 1
2 2 4 6 8 9
8 6 2 2 2 5
1 1 2 2 2 3
2 2 1 1 1 1
6 3 3 5 5 6
1 1 1 1 1 1
2 2 2 5 3 2
6 3 3 2 4 4
2 1 1 2 2 2
7 2 2 1 1 1
1 4 5 7 8 8
2 1 1 1 1 1
5 2 2 3 3 6
1 3 7 - - -
- 5 1 1 1 1
- 1 2 5 5 4
1 2 - - - -
7 1 2 6 - -
- 7 1 1 1 3
1 9 - - - -
T = { j 1 , j 2 ,···, j t }
the set of its transition positions. Two sequences S 1 and S 2 exhibit a match of the
transition seed P in positions x and y if, for 1 ≤ k ≤ m, S 1 [x−L Q +i k ]=S 2 [y−L Q +
i k ] and, for 1 ≤ k ≤ t, S 1 [x − L Q + j k ]=S 2 [y − L Q + j k ], or two residues S 1 [x − L Q +
j k ] and S 2 [y − L Q + j k ] are both pyrimidines or purines.
The analytical studies presented in this chapter can be generalized to transition
seeds in a straightforward manner. As a result, good transition seeds can be found
using each of the approaches discussed in Section 6.5.1. Hedera and Mandala that
were mentioned earlier can be used for transition seed design.