Exam_Project_PatternDetectionInProteins

[EngelsI]

No description provided.

[MichielStock]

Looks very nice, I see that you have a lot of general data structures typed with Any, e.g. Dict{Any,Any}. These give no error in Julia but make your code much slower because the functions can't specialize on them during compilation. Solving these is an easy way to improve performance. You can do it by providing type information, e.g. Dict{Char, Vector{Bool}}. In detect_motifs, you might store Tuples ("adfk", 1.0, 2.0), these will also specialize.

[jstaut]

Review (Jasper Staut)

README
Edit: "The protein sequences must be provided in FASTA format"

Introduction
I'm not sure I understand what "design" patterns are in proteins?

The data
Should the word "phages" also be in italics when saying "Pseudomonas phages" and "Staphylococcus phages"?
Edit: [...] related (compaired -> compared) to the other two sets

2 The Similarity_matrix function
I am a bit confused on the "tree based (evolutionary) multiple sequence alignment"
After reading part 3 below and the iterate function, I think I understand why it is evolutionary, but how is it tree based?

3 Multiple_alignment function
Maybe state somewhere that the consensus is made by taking only matching AA's and inserting a '-' otherwise
point 7. "Basis of the evolutionary algorithm." -> maybe reformulate that sentence?

[jstaut]

Also, a very nice and neat project! ^_^

[EngelsI]

Also, a very nice and neat project! ^_^

Thank you. The feedback was very helpfull!
I adjusted the text like you said. There were indeed some missing details to make it more easy to follow our train of thoughts.