Context: Changing which of the following BLAST parameters would tend to yield fewer search results? (a) turning off the low‐complexity filter; (b) changing the expect value from 1 to 10; (c) raising the threshold value; or (d) changing the scoring matrix from PAM30 to PAM70 Answer question

The answer is (c) raising the threshold value.

Here's why:

a) Turning off the low-complexity filter would actually yield more results, not fewer. This is because the filter removes sequences that have low complexity, such as simple sequence repeats. Without this filter, BLAST would return matches to these low complexity regions, increasing the number of results.

b) Changing the expect value from 1 to 10 would also yield more results. The expect value (E-value) is the number of hits one can "expect" to see by chance when searching a database of a particular size. Therefore, increasing the E-value would increase the number of hits that are considered significant, thus increasing the number of results.

c) Raising the threshold value would yield fewer results. The threshold value is the score that a match must reach to be considered significant. By raising this value, fewer matches will meet this criteria and thus fewer results will be returned.

d) Changing the scoring matrix from PAM30 to PAM70 would not necessarily yield fewer results. The scoring matrix is used to calculate the score for aligning two sequences. PAM30 and PAM70 are just two different matrices that might be used, and the choice between them would depend on the specific sequences being compared. It's not clear that one would consistently yield fewer results than the other.