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Sequence alignments

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 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 mark sequences using the checkboxes found in various places such as:

Once two or more sequences have been marked, the Align button in the green bar becomes available:

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:

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 rerun the alignment with fewer sequences, use the checkboxes in the "Annotation" section:

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

Related services

ClustalW (PIR)

Multiple sequence alignment

ClustalW (EBI)

Multiple sequence alignment


Align two sequences using the Smith-Waterman algorithm