Introduction To Bioinformatics

Homework Solutions for Introduction to Bioinformatics Course as Computer Science B.Sc. Student at Department of Computer Engineering, Sharif University of Technology

Homework Solutions for Introduction To Bioinformatics Course as Computer Science B.Sc. Student at Department of Computer Engineering, Sharif University of Technology

Fall 2022

Supervisors: Dr. Ali Sharifi Zarchi, Dr. Somayyeh Koohi

Description

This repository includes my homework and projects around Numerical Bioinformatics. There are some problems from Rosalind implemented in Python and Java. Also, a small project about dimension reduction and AML is included.

Table of Rosalind’s Problems

24 Rosalind problems listed below are implemented as homework.

Num Title
1 Computing GC Content
2 Complementing a Strand of DNA
3 Enumerating k-mers Lexicographically
4 Construct a Trie from a Collection of Patterns
5 Creating a Distance Matrix
6 Edit Distance Alignment
7 Global Alignment with Scoring Matrix and Affine Gap Penalty
8 Local Alignment with Scoring Matrix
9 Local Alignment with Affine Gap Penalty
10 Multiple Alignment
11 Inferring mRNA from Protein
12 Error Correction in Reads
13 Compute Distances Between Leaves
14 Compute Limb Lengths in a Tree
15 Implement AdditivePhylogeny
16 Implement UPGMA
17 Implement the Neighbor-Joining Algorithm
18 Implement SmallParsimony
19 Constructing a De Bruijn Graph
20 Genome Assembly Using Reads
21 Genome Assembly with Perfect Coverage
22 Assessing Assembly Quality with N50 and N75
23 Reconstruct a String from its Burrows-Wheeler Transform
24 Implement BWMatching