Sequence Comparison.pdf

6.7 Bibliographic Notes and Further Reading 117
Sampling approach is also studied in the paper of Preparata, Zhang, and Choi [168].
The spaced seeds reported in Section 6.5.2 are from the paper of Choi, Zeng, and
Zhang [48].
6.6
To our best knowledge, the idea of multiple spaced seeds is first used in Pattern-
Hunter [131] and is further studied in the papers of Li et al. [123], Brejovà, Brown,
and Vina˘r [29], Buhler, Keich, and Sun [34], Csürös and Ma [53], Ilie and Ilie [95],
Sun and Buhler [185], and Xu et al. [206].
Transition seeds are studied in the papers of Kucherov, Noè, and Roytberg [118],
Noè and Kucherov [153], Schwartz et al. [177], Sun and Buhler [186], Yang and
Zhang [208], and Zhou and Florea [216].
The vector seed is proposed in the paper of Brejovà, Brown, and Vina˘r [30] for
the purpose of protein alignment. In [31], Brown presents a seeding strategy that
has approximately the same sensitivity as BLASTP while keeping five times fewer
false positives.
Miscellaneous
For information on applications of the seeding idea to multiple sequence alignment,
we refer the reader to the papers of Flannick and Batzoglou [72] and Darling
et al. [54]. For information on applications of the seeding idea to other string matching
problems, we refer the reader to the papers of Burkhardt and Kärkkäinen [36],
Califano and Rigoutsos [37], and Farach-Colton et al. [65].