Match the trace with the sample

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Sandra Porter

DNA sequence traces are often used in cases where:

  1. We want to identify the source of the nucleic acid.
  2. We want to detect drug-resistant variants of human immune deficiency virus.
  3. We want to know which base is located at which position, especially where we might be able to diagnose a human disease or determine the best dose of a therapeutic drug.

In the future, these assays will likely rely more on automation. Currently, (at least outside of genome centers) many of these results are assessed by human technicians in clinical research labs, or DNA testing companies, who review these data by eye. (Yes, really!)

Today, you too, can be a data analyst and figure out what's happening with these traces.

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These traces came from PCR products that were obtained from bacterial cultures by Sanger dideoxy sequencing. The bacterial cultures were isolated by JHU students in 2004. Some questions might have multiple answers.

  • Which of these traces looks like it might have been generated from a mixed sample of DNA? (in this case, a mixed culture of bacteria.)
  • Which of these traces probably came from a pure culture of bacteria?
  • Which of these traces appears to contain positions with polymorphic bases? (Polymorphic means more than one form)
  • The Extra Credit Question: All of these traces came from independently-isolated bacteria and are not likely to be the same species. Even so, two of the traces appear to have very similar sequences. Why do you think this might be the case? You can use blastn to answer this, but be sure to adjust the parameters for short sequences.

And, if you want to download some of our data, you can see how to get it here.