Sequence alignments

Paste two or more identifiers or protein sequences in FASTA format into the sequence alignment form. This form can be accessed from all pages via the Align tab).

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 in the alignment form, you can instead mark sequences using the checkboxes found in various places such as:

• the UniProtKB, UniRef and UniParc search results,
• the sequences and sequence annotation sections in UniprotKB entries,
• the history of a UniProtKB entry,
• and in BLAST results.

Once two or more sequences have been marked, an option to align the marked sequences becomes available.

Once the sequences or identifiers have been submitted for alignment, a status page is shown. This page is reloaded in regular intervals until the alignment (ClustalW) is complete.

The final result page shows a colored version of the alignment. and allows download in ClustalW and FASTA format. To rerun the alignment with fewer sequences, use the checkboxes

If you want to use another sequence alignment service, click on retrieve rather than align, 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

SIM (ExPASy) Align two sequences using local similarity