Bioinformatics Course Programming Assignments

HW 1 - Semi-Global Alignment

In this assignment, I implemented a Semi-Global Alignment from scratch. I used PAM250 matrix for scoring (PAM250).
The program inputs two protein sequences, calculates the alignment score, and generates two modified sequences after alignment.

Sample Input:

HEAGAWGHE
PAWHEA

Sample Output:

20
HEAGAWGHE-
---PAW-HEA

HW 2 - Multiple Sequence Alignment

This assignment is about Multiple Sequence Alignment. The code consists of two main components. The first part involves the implementation of Star Alignment, a Multiple Sequence Alignment approach. The second part is a modification step designed to identify and replace blocks in the sequences after alignment.
The program first prompts the user to input the number of sequences. Subsequently, the sequences are provided as input. The output includes the final Multiple Sequence Alignment (MSA) score and aligned and modified sequences.

Sample Input:

4 
TYIMREAQYESAQ
TCIVMREAYE
YIMQEVQQER
WRYIAMREQYES

Sample Output:

51
-TYI-MREAQYESAQ
-TCIVMREA-YE---
--YI-MQEVQQER--
WRYIAMRE-QYES--

HW 3 - Profile

This assignment is about creating a profile for MSA and identifying the optimal subsequence of a given sequence.
The program first prompts the user to input the number of sequences. Subsequently, the sequences are provided as input. Then, it prompts the user to input a long sequence to find the best subsequence within it. Finally, it prints the best subsequence.

Sample Input:

4
T-CT
--CT
A-CT
ATCT
ATCCTATATCTTCTCTATACTATCCTTCA

Sample Output:

A-CT