I challenge myself to learn bioinformatics basics.
First goal is ELI5.
- What are those people doing in the lab? How do they know that was my drop of blood at the crime scene? I’d like to to how things are happening physically.
- I know DNA is a very fucking long sequence of ACTGs but how do you actually measure some thing like this without getting lost? How do you know xyz comes after abc? I mean you breakdown the chain into pieces for the sequencing, right?
- I recall when I was doing IBO in high school .. that you actually measure the “map distance” between genes that measures the probability of recombination. I know how to do the math given the numbers. But I know nothing more than that.
Then I want the informatik part:
- How do you represent the data.
- How do you make sense of the data.
And the bonus is that I want some heuristics for what I’m doing (meh, it’s operating systems, if there was a similarity it would be sci-fi. And no, I have no interest in the intellectual design bullshit)
and for those who waste their time reading this: enjoy watching how I suffer!
§ bookmarks
links
books (…well would be over-ambitious for me to list serious literatures as my beginner tutorials but … well…) I’m already scared.
- Biological sequence analysis - probabilistic models of proteins and nucleic acids (R.Durbin)
- An introduction to bioinformatics algorithms by Jones and Pevzner
- Molecular Evolution and Phylogenetics by Nei and Kumar
- Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory by Hein et al
MISC
BWT gives you free compressions.
https://en.wikipedia.org/wiki/Burrows%E2%80%93Wheeler_transform