Bioinformatics DNA Sequence Alignment Tool
Build a command-line tool that performs local sequence alignment between two DNA sequences using a from-scratch implementation of the Smith-Waterman algorithm, reading input from FASTA files via BioPerl and visualizing the alignment. Learners practice dynamic programming algorithms, BioPerl's sequence I/O, and scientific-computing style CLI tools.
- Estimate
- ~9h
- Steps
- 5
- Completed by
- 0
- Proposed by
- codeseed.app
BioPerl
Project roadmap
- 01
Parse FASTA input
~1.5hUse Bio::SeqIO from BioPerl to read two DNA sequences from FASTA files.
- 02
Implement the scoring matrix
~2.5hBuild the Smith-Waterman dynamic-programming score matrix with match/mismatch/gap penalties.
- 03
Implement traceback
~2hTrace back through the matrix from the highest score to reconstruct the optimal local alignment.
- 04
Format alignment output
~1.5hPrint the aligned sequences with match/mismatch indicators between them.
- 05
Add CLI options and tests
~1.5hSupport configurable penalty scores via CLI flags and test against known alignment examples.
Resources
Ready to build this?
Get a GitHub repo and start building. Your AI reviewer checks each step as you go.
Tech stack