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Sequence alignments

Last modified April 10, 2018


Select the Align tab of the toolbar to align two or more protein sequences with the Clustal Omega program (cf also this ClustalO FAQ):

  1. Enter either protein sequences in FASTA format or UniProt identifiers into the form field.
  2. Click the Run Align button.

The following kinds of UniProt identifiers are supported:

P00750 UniProtKB entry
P00750-2 UniProtKB entry isoform sequence
A4_HUMAN UniProtKB entry name
UPI0000000001 UniParc entry
UniRef100_P00750 UniRef entry

To limit the range within a sequence, append the range in square brackets to the identifier. For example, P00750[1-10] represents the first ten amino acids of P00750.

Instead of entering identifiers into the form, you can collect sequences by clicking into the checkboxes next to them. Once two or more sequences have been marked, the Run Align button becomes available:

Similarly, you can align the sequences that you have collected into your basket.

After you have submitted your data, a status page is shown. This page is reloaded in regular intervals until the alignment is complete. The final result page shows a colored version of the alignment and allows to download in Clustal format.

An alignment will display the following symbols denoting the degree of conservation observed in each column:

  • An * (asterisk) indicates positions which have a single, fully conserved residue.
  • A : (colon) indicates conservation between groups of strongly similar properties - scoring > 0.5 in the Gonnet PAM 250 matrix.
  • A . (period) indicates conservation between groups of weakly similar properties - scoring =< 0.5 in the Gonnet PAM 250 matrix.

Jobs have unique identifiers, which (depending on the job type) can be used in queries (e.g. to get the intersection of two sequence similarity searches). Job identifiers and the related data are kept for 7 days, and are then deleted.

To add sequences to your alignment, a text box just after the alignment results allows you to do so, in FASTA format:

To rerun the alignment with fewer sequences, check the box for "Result info" under "Display", and scroll down to the bottom of the page. Use the checkboxes to select the sequences you want to realign:

If you want to use another sequence alignment service, click on the Download instead of the Align button to download the sequences, or copy the sequences from the form in the result page.

'Annotation' and 'Amino acid properties' highlighting options are available on the left column. This allows to highlight key regions in the sequence alignment.

Related services

ClustalW (PIR)

Multiple sequence alignment

ClustalW (EBI)

Multiple sequence alignment


Align two sequences using the Smith-Waterman algorithm

UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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