Pairwise Protein Alignment

Perform global pairwise alignment of protein sequences using Needleman-Wunsch algorithm with BLOSUM and PAM matrices

Alignment Parameters

What is Pairwise Protein Alignment?

Pairwise protein alignment compares two amino acid sequences to identify regions of similarity using the Needleman-Wunsch global alignment algorithm. This method uses substitution matrices like BLOSUM62 to score amino acid matches and mismatches, accounting for evolutionary relationships and chemical properties of amino acids.

How to Use This Alignment Tool

Quick guide to align protein sequences:

  1. Enter two protein sequences (FASTA or plain text)
  2. Select scoring matrix (BLOSUM62 recommended)
  3. Adjust gap penalties if needed
  4. View optimal alignment with score and statistics

When to Use Pairwise Alignment

This tool is useful when you need to:

  • Compare two protein sequences for homology
  • Identify conserved functional domains
  • Analyze evolutionary relationships
  • Find optimal alignment for structure prediction
  • Assess sequence similarity and identity

Example Input

Sample sequences for alignment:

Seq 1: MKFLKFSLLTAVLLSVVFAFSSCGDDDDTGYLPPSQAIQDLLKRMKV
Seq 2: MKFLKGALLTAVLLSVVFAFSSCGDDDTGYLPPSQAIQDIIKRMKV

Try with your own sequences or use the Example button.

Example Output

Alignment showing matches (|), similarities (:), and gaps (-):

MKFLKFSLLTAVLLSVVFAFSSCGDDDDTGYLPPSQAIQDLLKRMKV
|||||.||||||||||||||||||||:|||||||||||:||.|||||
MKFLKGALLTAVLLSVVFAFSSCGDDDTGYLPPSQAIQDIIKRMKV

Results include alignment score and identity percentage.

FAQ

Q: Which scoring matrix should I use?
A: BLOSUM62 is recommended for most protein alignments. Use BLOSUM80 for closely related sequences or BLOSUM45 for distantly related sequences.

Q: What do the gap penalties mean?
A: Gap opening penalty is applied when starting a new gap, while gap extension penalty is for extending existing gaps. Typical values are -10 and -1.