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 | C | , | T | T | T | , | A | G | C |
| T | A | A | , | A | A | T | , | A | G | A |
| A | A | C | , | T | G | A | , | A | G | C |
| A | A | A | , | A | T | T | , | A | G | G |
| T | T | C | , | T | A | A | , | A | T | G |
| T | T | A | , | T | G | A | , | A | T | G |
| A | T | C | , | A | A | T | , | A | G | G |
| A | T | A | , | A | G | A | , | A | C | A |
| A | A | C | , | A | T | A | , | A | T | C |
| T | A | C | , | A | A | T | , | A | C | A |
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 | C | , | C | T | G | , | T | A | T |
| A | T | C | , | C | T | C | , | A | T | T |
| T | G | C | , | C | T | C | , | C | T | T |
| A | G | C | , | C | T | C | , | A | C | T |
| G | G | G | , | C | C | A | , | A | T | T |
| A | G | A | , | G | G | T | , | A | T | C |
| C | A | C | , | C | T | C | , | G | T | A |
| A | G | T | , | A | A | C | , | A | G | G |
| A | C | C | , | T | T | C | , | A | T | T |
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
| C | A | T | , | T | A | T | , | A | A | C | , | A | A | C |
| A | A | C | , | T | A | T | , | T | C | T | , | A | C | T |
| C | C | A | , | A | A | A | , | G | A | G | , | T | A | A |
| A | A | C | , | G | G | C | , | T | G | T | , | G | T | G |
| A | C | C | , | C | A | G | , | G | C | T | , | A | T | T |
| A | G | A | , | T | C | G | , | C | C | T | , | A | G | G |
| T | A | T | , | C | G | C | , | G | A | G | , | G | T | C |
| G | G | C | , | G | G | C | , | G | A | G | , | G | C | G |
| T | T | C | , | T | A | C | , | C | T | T | , | A | T | G |
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?
| A | C | T | , | G | T | A | , | A | C | A |
| A | A | G | , | C | A | G | , | C | A | C |
| A | A | G | , | C | G | A | , | T | G | A |
| A | T | A | , | T | G | A | , | C | C | G |