Question

Consider the following profile matrix: a: 0.4 0.3 0.0 0.1 0.0 0.9 c: 0.2 0.3 0.0 0.4 0.0 0.1 g: 0.1 0.3 1.0 0.1 0.5 0.0 t: 0.3 0.1 0.0 0.4 0.5 0.0 which of the following strings is a consensus string for this profile matrix? (select all that apply.)

Answer 1

A consensus string for the given profile matrix is obtained by selecting the nucleotide with the highest frequency at each position. Due to ties in the second and fifth positions, multiple consensus strings are possible, all starting and ending with 'a', and containing 'g' and 'c' in the third and fourth positions, respectively.

Step-by-step explanation:

To find a consensus string for a given profile matrix, we need to select the nucleotide with the highest frequency at each position of the profile. Taking each column in turn, we choose the nucleotide with the highest value. For the provided profile matrix, the consensus string would be:

• First position: 'a' (0.4)
• Second position: 'a' or 'c' or 'g' (all 0.3, tie)
• Third position: 'g' (1.0)
• Fourth position: 'c' (0.4)
• Fifth position: 'g' or 't' (both 0.5, tie)
• Sixth position: 'a' (0.9)

As there are ties in the second and fifth positions, there are multiple possible consensus strings. Strings will start with 'a', have 'g' in the third position, 'c' in the fourth, and 'a' in the sixth position. The second position could be 'a, 'c', or 'g', and the fifth position could be 'g' or 't'. Thus, multiple consensus strings match the profile, depending on how ties are resolved.