Cart 2

Pairwise Sequence Alignment Tool

Pairwise sequence alignment is a fundamental bioinformatics technique used to identify regions of similarity between two biological sequences. This tool supports both global and local alignment algorithms to meet different analysis needs.

Algorithm Features

  • Needleman-Wunsch Algorithm: Global alignment algorithm, optimal for sequences of similar length with high overall similarity
  • Smith-Waterman Algorithm: Local alignment algorithm, ideal for finding similar regions within sequences

Key Applications

  • Homology Detection: Identify evolutionary relationships between sequences
  • Functional Annotation: Predict function based on similarity to known sequences
  • Mutation Analysis: Compare sequences to identify variations and mutations
  • Phylogenetic Studies: Analyze evolutionary relationships between species

2. Input Two FASTA Format Sequences (Protein/Nucleic Acid):

Note: Long sequences may take longer to compute (20s+), please be patient

Sequence Count: 0 | Character Length: 0

3. Visualization Configuration:

User Guide

Input Requirements

  • Format: Standard FASTA format, each sequence starts with ">" followed by sequence identifier
  • Sequence Count: Exactly 2 sequences required for pairwise alignment
  • File Size: Total input should not exceed 200KB for optimal performance
  • Character Processing: Automatically filters spaces and non-standard characters
  • Sequence Types: Supports protein, DNA, and RNA sequences

Algorithm Comparison

Needleman-Wunsch (Global)
  • Purpose: Aligns entire sequences end-to-end
  • Best For: Similar length sequences with high overall similarity
  • Output: Complete alignment including gaps
  • Use Cases: Homology detection, evolutionary analysis
Smith-Waterman (Local)
  • Purpose: Finds best local similarity regions
  • Best For: Sequences with conserved domains or motifs
  • Output: Highest scoring local alignment
  • Use Cases: Domain identification, motif finding

Visualization Options

  • Start/End Position: Specify the range of alignment to display
  • Line Length: Control how many characters per line in the output
  • Line Spacing: Adjust vertical spacing between alignment blocks
  • SVG Export: Download high-quality vector graphics of the alignment

References

Needleman-Wunsch Algorithm:
Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology. 1970;48(3):443-53.

Smith-Waterman Algorithm:
Smith TF, Waterman MS. Identification of common molecular subsequences. Journal of Molecular Biology. 1981;147(1):195-7.