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- Bioinformatics for the terrified
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Bioinformatics as a science
Have you used BLAST? Is a BLAST search an experiment?
Here’s an example hypothesis: this yeast protein is encoding a function that’s conserved across eukaryotes. You could test that by running a BLAST search and see if you find it in other eukaryotes?
Therefore, you may be able to use BLAST to confirm or refute a hypothesis.
- But, would you think about controls?
- Record the parameters you use?
- Would you be able to replicate the results? The sequence database is constantly being updated, so it is likely you couldn’t replicate it.
When using bioinformatics methods reading the original paper will help you understand what it can be used for and, crucially, any limitations of the method.
Computational experiments still need controls, both positive and negative. Let’s consider a few of examples:
| Example | Positive control | Negative control |
| A method to predict protein structure | A sequence of a protein you know the structure off from x-ray crystallography | A random protein sequence |
| A method to identify tissue type from histology image | An image of known tissue type | An image of a blank slide |
| A method to predict gene structure from DNA sequence | A sequence of a gene with known structure | A scrambled sequence |
Some methods will always give an answer, regardless of its accuracy – it’s useful for you to know that kind of detail about a method! So it is important to read about the method prior to using it.
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After thinking about controls for using these kinds computational methods, are there any analyses you have done previously that you would do differently now? |
The application of bioinformatics involves using other people’s methods and sometimes creating your own. On the next page, we’ll discuss whether or not learning programming is essential.