Question

A consensus sequence identifies the base occurring most often at each position in the set of sequences. (a) Write out the consensus sequence of this (the nontemplate) strand. In any position where the base can't be determined, put a dash. (b) Which provides more information-the consensus sequence or the sequence logo? What is lost in the less informative method?

Answer 1

(a) Consensus sequence: A T C G T A - G (with dashes where base determination is unclear).

(b) Sequence logos provide richer detail, showcasing base frequencies and variability at each position, offering more insight than the simplified consensus sequence.

(a) The consensus sequence represents the most frequent base at each position in a set of sequences. If a position has multiple possibilities or if there's no clear base predominance, a dash ("-") is used.

For instance, a consensus sequence might look like this:

A T C G T A - G

Here, each letter represents the most frequent base found at that specific position across the sequences, and the dash indicates ambiguity or lack of a clear base.

(b) A sequence logo provides a graphical representation showing the frequency of nucleotides at each position. It offers more detailed information than a simple consensus sequence. What's lost in the consensus sequence is the quantification of base frequencies and their relative importance at each position, which a sequence logo visually portrays. The logo captures not only the most common base but also the proportional representation of other bases at that position, providing a richer understanding of sequence variability.

Answer 2

(a) We can see here that to write out the consensus sequence of the nontemplate strand, we identify the base occurring most often at each position in the set of sequences. If the base cannot be determined at a certain position, we put a dash.

What is consensus sequence?

It provides a straightforward representation of the most frequent bases at each position, giving a single sequence that is representative of the majority.

(a) To write out the consensus sequence of the nontemplate strand, we identify the base occurring most often at each position in the set of sequences. If the base cannot be determined at a certain position, we put a dash.

For example, let's say we have a set of DNA sequences:

Sequence 1: ATGCCG

Sequence 2: ATGACG

Sequence 3: ATGGCG

Sequence 4: ATGTTG

To determine the consensus sequence, we compare the bases at each position and choose the most frequent base. In this case, the consensus sequence would be:

Consensus Sequence: ATGGCG

The base "A" occurs most frequently at the first position, "T" at the second position, "G" at the third and fourth positions, "C" at the fifth position, and "G" again at the sixth position.

(b) The sequence logo provides more information than the consensus sequence. In a sequence logo, the height of each letter represents the frequency of occurrence of that base at a specific position, and the total height at each position represents the conservation level.