Sequence Comparison.pdf

78 4 Homology Search Tools
high-scoring segment pairs (HSPs). As for the gap extension of HSPs, a red-black
tree with diagonals as the key is employed to manipulate the extension process efficiently.
4.6 Bibliographic Notes and Further Reading
Twenty years ago, it would have been a legend to find similarities between two sequences.
However, nowadays it would be a great surprise if we cannot find similarities
between a newly sequenced biomolecular sequence and the GenBank database.
FASTA and BLAST were the ones that boosted this historical change. In Table C.2
of Appendix C, we compile a list of homology search tools.
4.1
The first linear-time suffix tree was given by Weiner [202] in 1973. A spaceefficient
linear-time construction was proposed by McCreight [135] in 1976. An online
linear-time construction was presented by Ukkonen [191] in 1995. A review of
these three linear-time algorithms was given by Giegerich and Kurtz [75]. Gusfield’s
book [85] gave a very detailed explanation of suffix trees and their applications.
Suffix arrays were proposed by Manber and Myers [134] in 1991.
4.2
The FASTA program was proposed by Pearson and Lipman [161] in 1988. It improved
the sensitivity of the FASTP program [128] by joining several initial regions
if their scores pass a certain threshold.
4.3
The original BLAST paper by Altschul et al. [7] was the most cited paper published
in the 1990s. The first version of BLAST generates ungapped alignments,
whereas BLAST 2.0 [8] considers gapped alignments as well as position-specific
scoring schemes. The idea of seeking multiple hits on the same diagonal was first
proposed by Wilbur and Lipman in 1983 [204]. The book of Korf, Yandell, and
Bedell [116] gave a full account of the BLAST tool. It gave a clear understanding
of BLAST programs and demonstrated how to use BLAST for taking the full
advantage.
4.4
The UCSC Genome Browser contains a large collection of genomes [104].
BLAT [109] is used to map the query sequence to the genome.
4.5