water (EBI)

water (EBI) performs local pairwise alignment of nucleotide and protein sequences using the Smith-Waterman algorithm to identify regions of similarity for functional, structural, or evolutionary inference.

Key Features:

• Smith-Waterman Algorithm: Implements the Smith-Waterman dynamic programming algorithm for optimal local alignment of nucleotide and protein sequences.
• EMBL-EBI Job Dispatcher integration: Integrated within the EMBL-EBI Job Dispatcher sequence analysis framework for coordinated sequence analysis workflows.
• Integration with EMBL-EBI resources: Interfaces with EMBL-EBI reference resources including UniProt, InterPro, ENA (European Nucleotide Archive), and Ensembl Genomes for comparative analyses.
• Scalability and data management: Updated to accommodate growing data volumes and large-scale analyses, as evidenced by performance during the COVID-19 pandemic.

Scientific Applications:

• Sequence Alignment: Produces precise local alignments of nucleotide or protein sequences to detect conserved regions and motifs.
• Functional Annotation: Supports annotation by comparing query sequences to entries in reference databases such as UniProt and InterPro.
• Evolutionary Studies: Enables inference of evolutionary relationships through pairwise sequence similarity analysis.
• Structural Biology: Informs structural prediction and comparative structural inference via detected sequence similarity.

Methodology:

The methodology employs the Smith-Waterman algorithm for local alignment, using dynamic programming to evaluate possible alignments and select the optimal match.