Is there such thing as a protocol in bioinformatics? Sure, why not. There are thousands of different ways that computers can be used to answer biological questions - each of which could certainly be called a protocol. A major benefit is that almost all of them are free.
The UBC bioinformatics links directory is a manually curated list of links to literally thousands of key web resources in bioinformatics. If you are looking for a bioinformatics protocol/recipe to solve a problem, this would be a great place to start your search.
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