BLAST

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BLASTN Protocols

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BLASTN Protocols

As we said earlier, most searches can be categorized as either mapping or exploring

searches. When sequences are expected to be nearly identical, you should use the

+1/-3 match-mismatch parameters, which have a target frequency of 99 percent

identity. Cross-species exploration requires a change in the scoring parameters and

word size. We like +1/-1 for both its simplicity and its 75 percent identity target fre-

quency. The choice of word size depends on balancing sensitivity and specificity.

The default word size of 11 is too risky; use 9, which corresponds to a little more

stringency than three identical amino acids because there’s no allowance for degener-

ate codons. The choice of gap costs depends on the size of the expected gap. For sim-

ulating sequencing errors, the gap costs should be uniform and relatively high, but

for modeling amino acid gaps or nucleotide hybridization bubbles, the cost of exten-

sion should be lower.

Mapping Oligos to a Genome

Many kinds of experiments, both molecular and computational, employ short nucle-

otide sequences called oligonucleotides, or just oligos (oligo is Greek for few). For

example, the polymerase chain reaction (PCR) is a routine laboratory procedure for

amplifying a specific nucleotide sequence from ...