seq-al

Aligning DNA and Protein sequences using Dynamic Programming

The following algorithms are implemented

Needleman-Wunsch Algorithm for global sequence alignment with linear gap penalties.
Modified Gotoh's Algorithm for global sequence alignment with affine gap penalties.
Smith-Waterman Algorithm for local sequence alignment with linear gap penalties.
Smith-Waterman Algorithm for local sequence alignment with affine gap penalties.

References:

Name		Name	Last commit message	Last commit date
Latest commit History 56 Commits
.gitignore		.gitignore
1_tracebacks.ipynb		1_tracebacks.ipynb
2_global_dp.ipynb		2_global_dp.ipynb
3_substitution_matrices.ipynb		3_substitution_matrices.ipynb
4_affine_gaps_global.ipynb		4_affine_gaps_global.ipynb
5_local_dp.ipynb		5_local_dp.ipynb
6_affine_gaps_local.ipynb		6_affine_gaps_local.ipynb
README.md		README.md
blosum50.csv		blosum50.csv
blosum62.csv		blosum62.csv
dna_identity.csv		dna_identity.csv
dna_transition_transversion.csv		dna_transition_transversion.csv
pam100.csv		pam100.csv
pam250.csv		pam250.csv
sequence_alignment.py		sequence_alignment.py