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We are still working on this page. Trees and tools will be added and opened gradually until the end of August, the date of the first complete version of this web site. You can find more about the schedule in "what's next ?"
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Catalog
Fitch/89
Fitch/extended
Subset
Taxonomy
Kitch/89
Kitch/extended
 
Tree of Life
PileUp/89
PileUp/extended
 
 

Click the purple button in the menu above or the purple bullet in the descriptive menu below. A Red bullet means the corresponding page is not release yet. If you click on it you will find a forecast of the release and the current state of the tool.

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Catalogs

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An terrific catalog is already available in the MEROPS web site and describes the distribution of peptidase clans and families among kingdoms of organisms (menu: catalog )
Description of the physiologic function and the pharmacologic target. Warning: companies need a license to use this nice facility from Rawlings N.D..
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Classification names from kindom to species at NCBI (menu: taxonomy)
This is a searchable index linked to the NCBI database, you may find the original form through the NCBI link. You can enter the name of superspecific taxa (e.g., Porifera) or the name of a particular organism (e.g., Thalarctos maritimus for the polar bear or polar bear itself).
Query:
Use query string as : complete match wild card search set of tokens
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Tree of life. This amazing web site gives you an overview of the systematic classification (menu: tree of life)
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Phylogenetic trees of serine proteases


Different phylogenetic trees of reduced sets of serine proteases are used. They were built from different methods applied to the same set

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Fitch-Margoliash Method - 89 S1 serine proteases (menu: Fitch/89)
The tree described in Krem et al. (1999, JBC, in press) was built from residues 16 to 245 of 89 non-redundant sequences of S1 proteases.
You can display residues from one to ten positions over the tree, make set from sub-branch and make logic operation on these sets to select specific residues shown ain aligned sequences or colored over the 3D structure.
Input: click sequence "leaves" and make sets
Output: specific residues displayed in alignment, or 3D-models

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Kitch Method - 89 S1 serine proteases (menu: Kitch/89)
Built from residues 16 to 245 according to the chymotrypsin numbering of 89 non-redundant sequences of S1 proteases.
Display residues from one to ten positions over the tree
Input: click sequence "leaves" and make sets
Output: specific residues displayed in alignment or 3D-models
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PileUp Method - 89 S1 serine proteases (menu: PileUp/89)
Built from residues 16 to 245 according to the chymotrypsin numbering of 89 non-redundant sequences of S1 proteases.
Display residues from one to ten positions over the tree
Input: click sequence "leaves" and make sets
Output: specific residues displayed in alignment or 3D-models
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Make your own phylogenetic trees of serine proteases

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Fitch or Kitch on subsets of S1 serine proteases (menu: Subset) You can make a subset of sequences and specified which residues have to be taken into account for the distance matrix calculus and for the tree building. The CGI program give you back a new alignment "edited" from the original done by clustal w. This alignment is ready to use for protdist then fitch or kitch.
Input: click sequence and specified residue positions
Output: distance matrix and tree by email

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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
Saint Louis, MO, U.S.A.

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