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Sequence Alignment Tool

Align two DNA sequences (A, C, G, T) using the Needleman-Wunsch algorithm, e.g., ATCG and AGTC.

Sequence Alignment Tool

ℹ️ Enter a DNA sequence using A, T, C, G (case-insensitive). Spaces are ignored. Only valid nucleotides are counted; invalid characters will trigger an error.
ℹ️ Enter a DNA sequence using A, T, C, G (case-insensitive). Spaces are ignored. Only valid nucleotides are counted; invalid characters will trigger an error.

Please enter two valid DNA sequences.

Alignment Result

Result will appear here

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Aligning...

Alignment History

    Alignment visualization will appear here

    About the Sequence Alignment Tool

    The Sequence Alignment Tool performs global pairwise alignment of two DNA sequences using the Needleman-Wunsch algorithm. This tool is ideal for molecular biology students, researchers, and educators analyzing sequence similarity.

    • Features:
      • Uses the Needleman-Wunsch algorithm for global alignment with scores: Match (+1), Mismatch (-1), Gap (-2).
      • Validates input to ensure only A, T, C, G (case-insensitive) are processed; ignores spaces.
      • Displays aligned sequences, alignment score, and counts of matches, mismatches, and gaps.
      • Provides a text-based visualization of the alignment.
      • Supports alignment history, result copying, and PDF export via LaTeX.
      • Keypad for easy input of A, T, C, G, with clear and backspace functionality.
    • Practical Applications: Useful in phylogenetics, homology detection, functional genomics, and sequence comparison.
    • How to Use:
      • Enter two DNA sequences (e.g., ATCG and AGTC) in the input fields or use the keypad.
      • Click "Align" to compute the global alignment.
      • View aligned sequences, score, and visualization; optionally copy or export to PDF.
      • Use "Clear" to reset or "⌫" to delete the last character from the active input.
    • Helpful Tips:
      • Input is case-insensitive; "atcg" and "ATCG" are equivalent.
      • Spaces are ignored; invalid characters (e.g., X, 1) trigger an error.
      • Click history items to reuse previous sequence pairs.
      • For large sequences, paste directly into the input fields.
      • Focus on one input field before using the keypad to specify which sequence to append to.
    • Examples:
      • Example 1: Similar Sequences:
        • Input: ATCG, AGTC
        • Result: Alignment: A-TCG / A-GTC, Score: 2, Matches: 3, Mismatches: 1, Gaps: 0
      • Example 2: Sequences with Gaps:
        • Input: ATTG, ATCGG
        • Result: Alignment: A-TT-G / ATCGG, Score: 1, Matches: 3, Mismatches: 0, Gaps: 2
      • Example 3: Invalid Input:
        • Input: ATCX, AGTC
        • Result: Error: Invalid characters detected (X).

    Align DNA sequences with ease and share or export results for your research or classroom!