Pairwise Align DNA

Global alignment of DNA sequences using Needleman-Wunsch algorithm with customizable scoring parameters

Scoring Parameters

Match Score2
Mismatch Penalty-1
Gap Penalty-1

What is Pairwise DNA Alignment?

Pairwise DNA alignment compares two DNA sequences to identify regions of similarity using the Needleman-Wunsch global alignment algorithm. This dynamic programming approach finds the optimal alignment by inserting gaps to maximize the alignment score based on matches, mismatches, and gap penalties.

How to Use This Pairwise Alignment Tool

Quick guide to align DNA sequences:

  1. Enter your two DNA sequences (FASTA or plain text)
  2. Adjust scoring parameters (match, mismatch, gap penalties)
  3. View the optimal global alignment with score
  4. Download or copy the alignment results

When to Use Pairwise Alignment

This tool is useful when you need to:

  • Compare two DNA sequences for similarity
  • Identify conserved regions between sequences
  • Find optimal alignment for primer design
  • Analyze sequence homology and evolution
  • Prepare sequences for phylogenetic analysis

Example Input

Sample sequences for alignment:

Sequence 1: GCATGCAGCC
Sequence 2: GATTACAGC

Try with your own sequences or use the Example button.

Example Output

Alignment result format:

Alignment Score: 8
GCATGCAGCC
G-AT-CAGC-
GATTACAGC-

Shows score and aligned sequences with gaps (-).

FAQ

Q: What is the Needleman-Wunsch algorithm?
A: A dynamic programming algorithm for global sequence alignment that finds the optimal alignment between two sequences.

Q: How do scoring parameters affect alignment?
A: Higher match scores favor identical bases, while penalty values control gap placement and mismatch tolerance.