IntroductionToBioinformatics

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