Question

A problem exists when comparing _____ sequences using the dot matrix method, namely, the _______

(a) small, amplification

(b) large, amplification

(c) small, high noise level

(d) large, high noise level

The question was posed to me in unit test.

This interesting question is from Methods in portion Pairwise Sequence Alignment of Bioinformatics

Answer 1

Correct choice is (d) large, high noise level

To explain I would say: In most dot plots, dots are plotted all over the graph obscuring identification of the true alignment. For DNA sequences, the problem is particularly acute because there are only four possible characters in DNA and each residue therefore has a one-in-four chance of matching a residue in another sequence.