BLAST

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Chapter 7: A BLAST Statistics Tutorial

melanogaster genome. On the other hand, it appears that looking for short—less

than 15 base-pair—cis-regulatory elements using either version of BLASTN with the

default parameters is unlikely to be successful.

So what was the unreported WU-BLASTN Expect? Let’s calculate it. With the data

in Table 7-3 and the previously calculated effective HSP length of 294, first calculate

m´ and n´ using the Perl functions

effectiveLengthSeq and effectiveLengthDB. Plug-

ging m´ and n´ together with the WU-BLASTN λ and k and a raw score of 125 into

the

rawScoreToExpect function gives an Expect of 281. Recall that the NCBI-BLASTN

Expect was 1e

-6

. That’s a 281-million-fold difference. BLAST is clearly parameter-

sensitive! Using the default parameters, you instructed NCBI-BLASTN to search for

short highly conserved regions, and it found one. WU-BLASTN, on the other hand,

is parameterized to look for large regions of relatively low percent identity. This

would be fine for cross-species searches of poorly conserved exons but is inappropri-

ate for finding oligos.

Using BLAST intelligently requires using the correct parameters for the task at hand

and not placing too much faith in the reported Expect. See the section on BLAST

protocols in Chapter 9 for practical