EMBOSS Water - Pairwise Sequence Alignment

EMBOSS Water uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment of two protein or nucleotide sequences.

Download Software

EBI FTP Download

EMBOSS FTP Download

Use this tool

STEP 1 - Enter your protein sequences

Enter or paste your first protein sequence in any supported format:

Or, upload a file:

AND

Enter or paste your second protein sequence in any supported format:

Or, upload a file:

STEP 2 - Set your pairwise alignment options

MATRIX
GAP OPEN
GAP EXTEND
OUTPUT FORMAT

STEP 3 - Submit your job

Be notified by email (Tick this box if you want to be notified by email when the results are available)

EMAIL:

TITLE: If available, the title will be included in the subject of the notification email and can be used as a way to identify your analysis

If you plan to use these services during a course please contact us.