Serine protease: Sequence Analyzer

Family ID	AC ID	Number trltor	Seq.Viewer	Score
Select	Keywords	Close to	Motif	Filter	Set operators
Save/read set	Align	Align custom	Window	AA freq	Specific

Set maker

1	Select a set from the entire sequence list

2	Select a set from the entire hidden list by keywords Protease, Organism, ac codes...

Evaluate identity and similarity scores between one sequence versus others
Choose the appropriate set of aligned sequence
Select a list sequences separated spaces, the first used as query
Select the window to compute the scores from residue to with the following reference for numbering (heavy chain of chymotrypsin by default)

Evaluate the similarity score with the selected substitution matrix

Select a set of sequences close to a sequence query
Choose the appropriate set of aligned sequence
Select a sequence as reference
Select the window to compute the scores from residue to with the following reference for numbering (heavy chain of chymotrypsin by default)
Minimal score of identity % or number of sequences with the best score of similarity
with the selected substitution matrix

Select a set of sequences from a motif
Choose a set of sequences
Range of motif search from to
with the following reference for numbering (heavy chain of chymotrypsin by default)
Enter the sequence of amino acids as reference

Select substitution matrix Allow gaps, gap openning penalty , gap extension penalty .

6	Select a set of sequences with specified constraints Choose the appropriate set of aligned sequence Select a sequence as reference . positions and constraints separated by spaces (ex: 57 H 102 D 195 S 189 D 225 Y)

7	Perform logical operations on sets
Set pad 1
Set pad 2
Set pad 3
Set pad 4
Set pad 5
	Set Operation Set

8	Read a set from a local file (in your computer) note :T2,G2 equivalent
	Enter the file name or find it with the browser

9	Save a set in a temporary file in the server (available during a 6h-period)
	Enter the file name or find it with the browser

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Go 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
Saint Louis, MO, U.S.A.