Scientists are often taught to structure
their experiments into four parts: the question
(hypothesis), the approach (experimental
design), the results (data), and the
interpretations (beliefs). This approach shows
that beliefs depend on the experiment's data.
Whether or not an experiment is capable of answering the question is
one way to separate good science from bad.
When setting up a BLAST experiment, the most important thing to
remember is "you get what you look
for." In other words, search parameters determine
what you find. For example, the BLASTN program from NCBI with the
default settings assumes that the alignments you are seeking are
nearly identical because the parameters (match +1, mismatch -3) have
a target frequency of 99 percent identity. If your experimental
question is "How many worm genes are related to my
favorite human gene," using the default parameters
would be foolish because the approach (looking for nearly identical
sequences) isn't expected to answer the question;
too many sequences have changed in the 500 million years that
separate worms and humans.