Needleman-Wunsch Algorithm • Full-Length
Forces end-to-end alignment. Best for closely related sequences of similar lengths. Useful for identifying overall structural homogeneity.
Smith-Waterman Algorithm • Regions
Finds localized regions of high similarity. Ideal for discovering conserved domains between distantly related or vastly different length sequences.
NCBI BLAST Mathematics • Fast Search
Heuristic local alignment using exact Karlin-Altschul statistics and linear gaps. Best for large database searching mimicking NCBI behavior.
Seed k-mer size
Neighbor score cutoff
Ungapped drop limit
E-value significance
Effective database length in residues