Question

Use the Overlap - Layout - Consensus (OLC) method to generate a consensus sequence for the set of reads below. There is no minimum overlap requirement for this assembly. Be sure to show all of the steps involved including the scores for each edge of the overlap graphs in the assembly. Report all of these steps and the final consensus sequence you recover from your assembly. As I did in the lecture, it will likely be easiest to draw the graphs by hand. If you make it by hand, just upload a photo of your results to D2L.

Reads:
GTTCACGT
TCGTATCCGT
ACGTCGTAT

Answer 1

To assemble a consensus sequence using Overlap - Layout - Consensus (OLC), overlaps between the given reads GTTCACGT, TCGTATCCGT, and ACGTCGTAT are identified, an overlap graph is constructed, then the consensus sequence GTTCACGTATCCGT is derived.

Step-by-step explanation:

To assemble a consensus sequence using the Overlap - Layout - Consensus (OLC) method for the given set of reads (GTTCACGT, TCGTATCCGT, ACGTCGTAT), we need to determine the overlaps between the reads, construct an overlap graph to visualize the layout, and then derive the consensus sequence.

First, we look for overlaps between every pair of reads:

• GTTCACGT and TCGTATCCGT overlap with 'TCGT'.
• TCGTATCCGT and ACGTCGTAT overlap with 'CGTAT'.
• GTTCACGT and ACGTCGTAT do not overlap directly.

Now we score each edge of the overlap graph:

• The overlap 'TCGT' between the first and second reads scores 4 (1 for each matching base).
• The overlap 'CGTAT' between the second and third reads scores 5.

Using these overlaps, we can construct an overlap graph and the layout would show that the first read connects to the second, and the second to the third.

Finally, the consensus sequence is recovered by merging the sequences at their overlaps:

• GTTCACGT + TCGTATCCGT -> GTTCACGTATCCGT
• GTTCACGTATCCGT + ACGTCGTAT -> GTTCACGTATCCGT

The final consensus sequence from the assembly is GTTCACGTATCCGT.