ammahmoudi / introductiontobioinformatics

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

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