alignment
Definition
Alignment in bioinformatics is the process of arranging DNA, RNA, or protein sequences to identify regions of similarity that may indicate functional, structural, or evolutionary relationships. Sequence alignment can be pairwise (comparing two sequences) or multiple (comparing three or more sequences). Algorithms like BLAST, Smith-Waterman, and Needleman-Wunsch use scoring matrices and gap penalties to optimize alignments. Alignment is fundamental for identifying homologous genes, predicting protein structure, detecting conserved domains, phylogenetic analysis, and variant calling. Quality alignment is critical for downstream analyses including gene annotation, comparative genomics, and understanding molecular evolution across species.
Visualize alignment in Nodes Bio
Researchers can visualize alignment results as networks where nodes represent sequences or genes and edges indicate alignment scores or similarity metrics. This enables identification of sequence clusters, visualization of homology relationships across species, and mapping of conserved domains. Network views help reveal patterns in large-scale comparative genomics studies and identify evolutionary relationships that may not be apparent in traditional alignment viewers.
Visualization Ideas:
- Sequence similarity networks showing homologous gene families across species
- Alignment score heatmaps converted to network graphs for identifying conserved protein domains
- Phylogenetic relationship networks derived from multiple sequence alignments
Example Use Case
A pharmaceutical team investigating drug resistance mechanisms in cancer aligns tumor protein sequences from 50 patients against reference databases. They identify mutations in the kinase domain of EGFR across multiple patients. By visualizing alignment scores as a network, they discover three distinct mutation clusters, each associated with different resistance profiles to tyrosine kinase inhibitors. This network view reveals that patients with similar mutation patterns respond similarly to treatment, enabling stratification for personalized therapy approaches.