Color Align Properties

Color Align Properties
Colour a protein alignment by residue physicochemical property group
Aligned Sequences

FASTA or GDE format. All sequences must be pre-aligned (equal length including gaps). Input limit: 200,000,000 characters.

Options
Starting Positions (optional)

Comma-separated starting positions to offset the per-sequence residue counter. Defaults to 0 for all sequences when left empty.

💡 Quick Summary

Color Align Properties accepts a group of aligned sequences in FASTA or GDE format and colours each residue by its biochemical property group (ClustalX-style). Small aliphatic residues are yellow, aromatics lavender, sulphur-containing pink, hydroxyl amber, positively charged blue, negatively charged coral, amide green, and proline violet.

📋 How to Use
  1. Paste pre-aligned sequences in FASTA or GDE format into the textarea. All sequences must be the same length (gaps included). Input limit: 200,000,000 characters.
  2. Set residues per line — controls how many alignment columns are shown per block row (default: 80).
  3. Set the consensus threshold — the minimum percentage of sequences that must share residues from the same property group at a column for colouring to be applied (default: 100%).
  4. Choose the colour mode: Background fills residues with the property colour; Text colours the characters instead (useful for printing on white paper).
  5. Optionally enter starting positions as comma-separated integers to offset the per-sequence position counter (e.g. 0, 200, 0, -1).
  6. Click Run. A colour key is shown above the alignment. Use Copy to copy the plain-text alignment.
🧮 Formulas & Logic
Property check
Count of sequences whose residue at a column belongs to the same property group ÷ total sequences ≥ threshold → property colour applied
Position counter
Increments by the number of non-gap characters (not - or .) in each displayed block for each sequence
📊 Result Interpretation
Yellow (GAVLI)

Small non-polar aliphatic residues: Glycine, Alanine, Valine, Leucine, Isoleucine.

Lavender (FYW)

Aromatic residues: Phenylalanine, Tyrosine, Tryptophan.

Light pink (CM)

Sulphur-containing residues: Cysteine, Methionine.

Amber (ST)

Small polar hydroxyl residues: Serine, Threonine.

Blue (KRH)

Positively charged residues: Lysine, Arginine, Histidine.

Coral (DE)

Negatively charged residues: Aspartate, Glutamate.

Green (NQ)

Polar amide residues: Asparagine, Glutamine.

Violet (P)

Imino residue: Proline.

No colour

Gap, stop codon (*), or residue not belonging to any of the above groups at ≥ threshold %.

Position numbers

Printed at the end of each row — the cumulative count of non-gap residues up to that point.

🔬 Applications
  • Visualising physicochemical conservation patterns in a multiple protein sequence alignment
  • Identifying positions where biochemical character is conserved even when exact residues differ
  • Producing publication-quality ClustalX-style coloured alignment figures
  • Comparing property distribution across different regions of a protein family alignment
  • Highlighting functionally important residue positions by their biochemical class
⚠️ Common Mistakes & Warnings
Sequences must be pre-aligned and equal length

This tool does not perform sequence alignment. All input sequences must already be aligned and must have identical lengths (including gap characters).

Designed for protein alignments

The property colour scheme is based on amino acid physicochemical groups. It is not meaningful for DNA or RNA alignments.

Sequence titles are truncated to 20 characters

Only the first 20 characters of each FASTA title are used for display. Ensure the first 20 characters of each title are distinct enough to identify the sequence.

❓ Frequently Asked Questions

How does property colouring differ from conservation colouring?
Conservation colouring (Color Align Conservation) highlights columns where the same residue or similar residues appear. Property colouring colours every residue by its biochemical group regardless of what the other sequences contain — unless a consensus threshold is set, in which case colour is only shown when ≥ threshold % of sequences at that column share the same property group.
What does the consensus threshold do here?
At 100 % (default), a residue is coloured only when every sequence at that column has a residue from the same property group. Lower the threshold (e.g. 80 %) to colour columns that are group-conserved in most sequences. At very low thresholds, almost every non-gap residue will be coloured.
Why does the position counter start at 0?
By default, position numbering starts at 0 for all sequences. To begin at a different position — for example to match the numbering of a reference sequence — enter the starting values in the Starting Positions field, one per sequence separated by commas.
Can I change which residues belong to each colour group?
No — the property groups are fixed to the standard ClustalX scheme used by the Sequence Manipulation Suite. Use Color Align Conservation if you need custom similarity groups.
Color Align Properties — logic ported from the Sequence Manipulation Suite (Paul Stothard, University of Alberta).