July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 5: BLAST
Once HSPs are organized into consistent groups, they can be evaluated with a final
threshold based on the entire search space and corresponding to the value of E set for
the search. You can read more about this topic in Chapter 4. BLAST reports any
alignment or group of alignments that meets the E requirement.
Implementation details
This chapter initially described BLAST as having three phases: seeding, extension, and
evaluation. In reality, BLAST isn’t so straightforward. There are two rounds of exten-
sion and evaluation: ungapped and gapped. Gapped extension and evaluation are
triggered only if ungapped alignments surpass the ungapped thresholds. In other
words, to find a gapped alignment, you must first find a reasonable ungapped
alignment.
In NCBI-BLAST, the command line parameter
-e sets the final threshold. The value
for the alignment threshold is set by the software and isn’t a user-definable parame-
ter. You can find the value for E in the footer. For example, if E is set with
-e 1e-10,
E is reported as follows:
Number of sequences better than 1.0e-10: 4
The value for the alignment threshold and its gapped equivalent are displayed
respectively as S1 and S2 with the raw score listed first. Note that the ungapped
threshold is quite a bit lower than the gapped ...
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