July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 5: BLAST
You’ll also find several BLAST derivatives and BLAST wrappers (scripts that run
BLAST in a specialized way) with names such as PSI-BLAST, PHI-BLAST, Mega-
BLAST, BLASTZ, XBLAST, MPBLAST, HT-BLAST, and GENE-BLAST. This
book—and especially this chapter—deals primarily with the five traditional pro-
grams. If you are familiar with the details of these algorithms, you will have a solid
foundation for understanding the variants.
The BLAST Algorithm
The search space between two sequences can be visualized as a graph with one
sequence along the X-axis and the other along the Y-axis (Figure 5-1). Each point in
this space represents a pairing of two letters, one from each sequence. Each pair of
letters has a score that is determined by a scoring matrix whose values were deter-
mined empirically. (See Chapter 4 for more about scoring matrices.) An alignment is
a sequence of paired letters that may contain gaps (See Chapters 3 and 4 for more
about gaps). Ungapped alignments appear as diagonal lines in the search space, and
the score of an ungapped alignment is simply the sum of the scores of the individual
letter pairs. Alignments containing gaps appear as broken diagonals in the search
space, and their score is the sum of the letter pairs minus the gap costs, which usu-
ally ...
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.