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Computational Biology Lab Guide

This lab manual outlines 15 programming assignments for a computational biology algorithms course. The assignments include implementing string matching algorithms like KMP; performing local sequence alignment with dynamic programming and tools like FASTA and BLAST; calculating distances like Hamming and Edit; modeling hidden Markov models with Forward and Backward algorithms; building suffix trees; cellular automata, agent-based, and PDE modeling; protein folding; and predator-prey simulations. The course aims to give students hands-on experience with fundamental algorithms in computational biology.

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138 views1 page

Computational Biology Lab Guide

This lab manual outlines 15 programming assignments for a computational biology algorithms course. The assignments include implementing string matching algorithms like KMP; performing local sequence alignment with dynamic programming and tools like FASTA and BLAST; calculating distances like Hamming and Edit; modeling hidden Markov models with Forward and Backward algorithms; building suffix trees; cellular automata, agent-based, and PDE modeling; protein folding; and predator-prey simulations. The course aims to give students hands-on experience with fundamental algorithms in computational biology.

Uploaded by

hifzan786
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd

National Institute of Technology, Uttarakhand

B. Tech (Computer Science & Engineering) Spring Semester 2016


Fundamental Algorithms in Computational Biology CSL403
Lab Manual
1. Implement the KMP (Knuth-Morris-Pratt) string matching algorithms.
2. Program to find the local alignment score using Dynamic Programming for DNA
sequences.
3. Implementation of FASTA with DNA sequences.
4. Implementation of BLAST with two RNA sequences to perform the local alignment.
5. Program to implement Hamming Distance
6. Program to implement Edit Distance.
7. Program to evaluate the probability of observations generated by the model.
8. Implementation of Forward method of HMM.
9. Implementation of Backward method of HMM.
10. Write a program to sketch a Suffix Tree of the sequence.
11. Write a program to design a Cellular Automata based Modeling.
12. Implementation of Agent Based Modeling Techniques.
13. Write a program to design Partial Differential Equations based Modeling.
14. Implementation of protein sequence in 3D structure (Protein Folding).
15. Program to implement Fox-Rabbit Predation.

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