13: Bioinformatics
Students analyze GAPDH DNA and protein sequences using BLAST, interpret alignment scores, and use bioinformatics databases to compare sequences across species.
Degenerate Primer Codes from Sequence Alignments
Click to show Degenerate Primer Codes from Sequence Alignments example problem
| A | T | G | , | A | G | A | , | G | C | T |
| T | G | A | , | G | G | C | , | G | C | C |
| G | G | A | , | A | G | T | , | G | C | C |
| G | C | C | , | C | G | T | , | G | C | T |
| G | T | G | , | A | G | C | , | G | C | C |
| A | C | A | , | C | G | T | , | G | C | C |
| T | C | G | , | A | G | A | , | G | C | T |
| T | G | T | , | C | G | T | , | T | C | C |
| A | T | C | , | C | G | A | , | C | C | T |
| T | G | T | , | A | G | A | , | C | C | C |
What is the arbritrary sequence code for degenerate primer design in the table above?
You may include a comma every 3 letters, but do NOT include any extra commas or spaces in your answer.
Consensus Sequences from Simple Alignments (Fill in the Blank)
Click to show Consensus Sequences from Simple Alignments (Fill in the Blank) example problem
| A | G | G | , | T | A | T | , | A | A | A |
| A | G | C | , | C | C | A | , | G | A | C |
| A | A | C | , | T | A | G | , | G | G | C |
| G | G | A | , | T | A | A | , | G | A | C |
| A | G | C | , | T | A | A | , | G | A | G |
| A | G | C | , | G | T | A | , | C | C | C |
| C | C | T | , | A | A | C | , | G | A | C |
| A | T | C | , | T | G | A | , | T | T | T |
| T | G | C | , | T | A | A | , | G | A | C |
What is the consensus sequence for the table above?
you may include a comma every 3 letters, but do not include any extra commas or spaces in your answer.
Consensus Sequences from Tables (Fill in the Blank)
Click to show Consensus Sequences from Tables (Fill in the Blank) example problem
| T | A | A | , | T | C | A | , | C | A | C | , | C | C | T |
| G | G | G | , | T | C | A | , | A | T | T | , | C | C | G |
| T | A | T | , | A | C | C | , | C | C | C | , | T | C | C |
| T | G | G | , | A | T | G | , | T | C | A | , | G | T | G |
| G | G | T | , | A | T | C | , | A | C | C | , | G | T | T |
| T | G | G | , | A | C | C | , | T | C | G | , | C | A | G |
| T | T | C | , | G | T | G | , | T | G | A | , | C | T | C |
| G | A | C | , | A | T | T | , | G | A | T | , | C | A | G |
| A | G | G | , | T | T | C | , | T | C | G | , | C | T | A |
What is the consensus sequence for the table above?
you may include a comma every 3 letters, but do not include any extra commas or spaces in your answer.
Consensus Sequences from Alignments (Multiple Choice)
Click to show Consensus Sequences from Alignments (Multiple Choice) example problem
What would be the consensus sequence for the following aligned sequences?
| G | G | G | , | G | G | T | , | A | G | C |
| G | C | C | , | A | C | T | , | T | C | A |
| G | T | G | , | C | T | G | , | C | G | A |
| G | G | A | , | A | T | C | , | T | T | T |
Gene Trees from Distance Matrices (5 Leaves, 5 Choices)
Click to show Gene Trees from Distance Matrices (5 Leaves, 5 Choices) example problem
| taxa | Bellen | Kraken | Narloc | Rynoth | Xeraph |
|---|---|---|---|---|---|
| Bellen | × | 38 | 38 | 58 | 56 |
| Kraken | 38 | × | 6 | 48 | 52 |
| Narloc | 38 | 6 | × | 56 | 54 |
| Rynoth | 58 | 48 | 56 | × | 22 |
| Xeraph | 56 | 52 | 54 | 22 | × |
The table above represents a distance matrix for the following taxa: Bellen, Kraken, Narloc, Rynoth, Xeraph. The values in the matrix correspond to the genetic distances between pairs of taxa.
For example, the distance between taxon Bellen and taxon Kraken is 38. Distances are symmetric, meaning that both the distance between taxon Kraken and taxon Narloc is 6 and the distance between taxon Narloc and taxon Kraken is 6.
Using this distance matrix, determine the most appropriate gene tree that accurately reflects the relationships and distances between these taxa.
Hint: taxa with smaller distances are more closely related. Look for clusters that best match the smallest distances.