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How do you align sequences?
There are 2 different ways to select the sequences to align. Write or paste their accession numbers in the dialog box or select them directely from the following list of serine proteases.

There are three different ways to get alignment of sequences. If you submit yourself sequences to an alignment program you may choose your own parameters for gap openning and extension penalties and substitution matrices. If you use ready-to-use alignment parameters are fixed.

You can select the accession numbers of the sequences to edit and submit them to Clustal W (Washington University).
You can use our ready-output from Clustal W and select the accession numbers of the sequences to edit.
You can use the HSSP multialignment and select the accession numbers of the sequences to edit.

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Alignment got from Clustal W 1.7 / HSSP / PFAM
Only the catalytic domain isused for this alignment
Parameters used: weigth matrix=blosum, Gap opening=10.0, extension=0.05

Write the reference protein used for the numbering of residues (bovin chymotrypsin by default).


Write the accession numbers of the selected sequences (<100), separated by a space.


Select the window for alignment editing from residue to (heavy chain of chymotrypsin by default)

Select the type of display:
horizontal, vertical
black&white
aa properties color-coded
identity (red %) and similarity (blue % for matrix and corresponding threshold ) color-coded

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Submit your sequence to Clustal W at Washington University ... coming soon!

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Go to the Washington University in St Louis
Go to the School of MedicineGo to the Department of Biochemistry and Molecular Biophysics

Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
St. Louis, MO, U.S.A.

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