Color Align Properties

Visualize aligned protein sequences with colors based on amino acid properties - hydrophobic, polar, charged, and aromatic residues.

Colored Alignment

Color Legend

What is Color Align Properties?

Color Align Properties is a visualization tool that colors protein sequence alignments based on amino acid biochemical properties. It helps identify conserved regions, functional domains, and structural motifs by highlighting residues with similar properties.

How to Use This Tool

Visualize your protein alignments:

  1. Paste aligned protein sequences in FASTA format
  2. Select a color scheme (properties, hydrophobicity, etc.)
  3. Adjust conservation threshold if needed
  4. View colored alignment below

When to Use

This tool is valuable when you need to:

  • Identify conserved functional regions
  • Visualize hydrophobic patches
  • Find charged residue clusters
  • Prepare figures for publications

Color Schemes

Properties: Hydrophobic (yellow), Polar (green), Positive (blue), Negative (red), Aromatic (purple)

Hydrophobicity: Gradient from hydrophobic (red) to hydrophilic (blue)

Polarity: Nonpolar (yellow) vs Polar (blue/red)

Example Output

Aligned sequences with colored residues:

Seq1: MSK...
Seq2: MTR...

Colors indicate amino acid properties.

FAQ

Q: What alignment formats are supported?
A: FASTA format with aligned sequences (including gaps marked as '-').

Q: Can I export the colored alignment?
A: Yes, download as HTML to preserve colors, or copy the plain text version.