Sequence-Align

This is a Repo consists of two modules:

1. A data parser that streams the UniProt protein sequence.
2. A Sequence Alignment tool implementing the Needleman-Wunsch algorithm.

SeqAlign

See SeqAlign.py.

Pairwise sequence global alignment to find out their optimal alignment score, optimal alignment, and the corresponding sequence identity.

• Adjustable substitution score matrix (default BLOSUM62)

CompareProteinSeq

See CompareProteinSeq.py.

Fetch and parse the UniProt protein sequence (FASTA format) with this url format: https://rest.uniprot.org/uniprotkb/${seq_id}.fasta.

Experiement the sequence global alignment by calling the SeqAlign given a compare set containing the protein sequence name (id).

Experiments

To get the comparing results, execute $python __main__.py.

Future Work/ Improvements

• Implement pairwise sequence local alignment using Smith–Waterman algorithm.