Globin family
Compare representative globin sequences.
Sequence Alignment Viewer
FigranView a multiple sequence alignment and download it as a publication figure.
- FASTA, Clustal or Stockholm
- ESPript-style shading
- Free SVG and 300 DPI PNG
Sequence alignment viewer examples
Explore a sequence alignment figure, then load it into the viewer.
SH3 domains with β-strands
Compare a set of SH3 domains.
C2H2 zinc fingers with sequence logo
Inspect conserved residues in zinc fingers.
tRNA alignment
Explore a nucleotide alignment of transfer RNAs.
Protein kinase domains
Explore 37 kinase domains, starting with the Gly-rich loop.
Insulin across species
Compare insulin sequences across species.
How to view a multiple sequence alignment
Create a publication figure from an existing alignment.
1Paste or import
Paste an aligned file or import it from your computer.
2Choose sequences
Select the visible rows and reference sequence.
3Style the figure
Choose colors, tracks and optional secondary structure.
4Download
Download PNG or SVG for a manuscript or multi-panel figure.
Read an alignment figure
Color and tracks make conserved positions and structural features easier to inspect.
- 1Identical column
- 2Equivalent residues
- 3Numbering
- 4Secondary structure
Consensus and conservation
The consensus is the most common residue in each column; the conservation bar includes gaps in its denominator.
Add a sequence logo
A sequence logo shows the information content in bits with a small-sample correction.
References: Schneider & Stephens, 1990 · Robert & Gouet, 2014
Alignment coloring schemes
Choose a coloring scheme to emphasize conservation or residue properties.
| Scheme | Rule | Use | Source |
|---|---|---|---|
| ESPript style | Identical columns are red; equivalent residues are boxed. | Publication figures | ESPript user guide |
| Clustal X | Colors depend on column composition and residue type. | Compare residue properties | Jalview documentation |
| Percent identity | Blue shades show the fraction matching the consensus. | Find conserved positions | Jalview documentation |
| BoxShade style | Identical residues are black; similar residues are gray. | High-contrast print figures | BoxShade documentation |
| BLOSUM62 score | Shades identify positive substitution scores against the consensus. | Inspect substitutions | NCBI BLOSUM62 |
| Nucleotide | A, C, G and T/U have different colors. | DNA or RNA alignments | Jalview documentation |
| Zappo | Colors group residues by physicochemical properties. | Compare residue properties | Jalview documentation |
| Taylor | Each amino acid has a characteristic color. | Distinguish amino acids | Jalview documentation |
| Hydrophobicity | Colors follow the Kyte–Doolittle hydropathy scale. | Inspect hydropathy | Kyte and Doolittle, 1982 |
Sequence alignment viewer FAQ
Which alignment formats can I open?
Open aligned FASTA (including A2M/A3M), Clustal, Stockholm or PHYLIP. Convert MSF and NEXUS to FASTA first.
Can this tool align my sequences?
No. Align sequences with Clustal Omega, MAFFT or MUSCLE before importing them.
How do I make an ESPript-style figure?
The default ESPript-style coloring uses the %Equivalent groups HKR, DE, STNQ, AVLIM, FYW and PGC at a 0.7 threshold. Identical columns are red; equivalent residues are red with a blue frame. This style is independently implemented.
What do the Clustal X colors mean?
Clustal X colors depend on the residue type and each column’s composition; see the coloring table above.
How is conservation calculated?
Conservation is the fraction matching the most common residue, with gaps included in the denominator.
How do I add secondary structure from a PDB file?
Upload a PDB or mmCIF file and select a chain that matches the reference sequence. The viewer reads structure records and does not predict structure.
Can I make a sequence logo?
Yes. Enable the sequence logo track to display information in bits with a small-sample correction. For a standalone logo from sites or a motif matrix, use the Sequence Logo Generator.
Is my alignment uploaded?
No. Your alignment and structure files stay in your browser. NCBI Multiple Sequence Alignment Viewer processes submitted data on its service.
Is there an online version of Jalview?
Yes. JalviewJS runs in a browser; this viewer focuses on alignment figures.