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):

Enter either protein sequences in FASTA format or UniProt identifiers into the form field.
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:

UniProtKB, UniRef and UniParc search results
the Sequences and Sequence annotation sections in UniProtKB entries
the history of a UniProtKB entry
BLAST results

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:

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 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

SSEARCH (PIR)

Align two sequences using the Smith-Waterman algorithm