https://github.com/janisz/bioinformatics

Code for bioinformatics course
https://github.com/janisz/bioinformatics

Last synced: 22 days ago
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Code for bioinformatics course

• Host: GitHub
• URL: https://github.com/janisz/bioinformatics
• Owner: janisz
• License: mit
• Created: 2016-01-19T20:37:30.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2016-01-22T20:51:29.000Z (almost 9 years ago)
• Last Synced: 2023-03-23T07:48:13.445Z (over 1 year ago)
• Language: R
• Size: 4.88 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Bioinformatics

Code for bioinformatics course

1. Create the function that extracts cartesian coordinates of atoms from PDB file and calculates the distances between all CA atoms in the protein structure. [Code](coordinates.r)

2. Create an application that will take as an input two DNA sequences (verification!) Based on their lengths it will calculate their global or semiglobal alignment. [Code](psa.r)

3. Implement program in R that will: [Code](clustering.r)

  * calculate correlation between provided data (matrix); choose the least correlated data

  * perform PCA on chosen data; distinguish data with the highest variance

  * Apply K-means clustering algorithm to the chosen data with the highest variance

  

4. Implement in R either Malthus or Predator-Prey model [Code](malthus.r)