I am a third year bioinformatics student and would like to apply my knowledge from an introductory course in Optimization Methods to some problems in the field of genomics or bioinformatics.

Do you know any optimization problems in this context that a beginner in OR could solve?

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    $\begingroup$ I suppose you googled bioinformatics optimization? The 2nd link I get is "Math 574 -- Optimization Models in Computational Biology" math.wsu.edu/math/faculty/bkrishna/Math574_S08.html which seems to have a lot of material. Plenty more on other search results. $\endgroup$ Nov 24 '20 at 16:03
  • $\begingroup$ Yes I did, but I figured, since I am not particularly proficient in the field of OR, it might be worth it to ask people to recommend something they see fit. Anyway thanks for your answer! $\endgroup$
    – Klumpi
    Nov 24 '20 at 16:08
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    $\begingroup$ I'd at least start by going through the course material in my comment's link. $\endgroup$ Nov 24 '20 at 16:37
  • $\begingroup$ What is the motivation to ask this question OR and not in bioinformatics? From the description it might be more suitable for bioinformatics questions. $\endgroup$
    – SimonT
    Nov 25 '20 at 13:02

The simplest problem I can come up with. You have three operations: insertion, deletion and replacement and they are assigned weights: i,d,r. How to transform one string (say AGCT) into another (say TGCAT) with minimum total weight. One way to do this: AGCT->TGCT->TGCAT. One replacement and one insertion; total weight: r+i. It can be easily solved by dynamic programming. The strings are genomes or chromosomes, and the operations are gene mutations.


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