menu also at the end of this page home Overview links search toolbox.html browser setup help contact us about Help and references Correlation with function Tour and Tutorials Evolutionary trees Substrate and inhibitor catalogs Mutations Structure analyzer Sequence analyzer Structure index Family and sequence index horiz_blue.gif
We are still working on this page. 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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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

Click the cyan button in the menu above or the cyan bullet in the descriptive menu below. A Red bullet means the corresponding page is not yet released. If you click on it you will find an estimate of the release date and its current state of development.

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Family / Clan Identify

Go to page bottom Identify if a sequence could be a serine protease (menu: family ID)
Input: amino-acid sequence
Output: clan and family names and accession number of the closest sequence
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Go to page bottom AC Identify
Go to page bottom Identify the name of a sequence from its accession number (menu: AC ID)
Input: list of accession numbers
Output: list of corresponding names, organism and other associated accession numbers
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Go to page bottom Number translator
Go to page bottom Give the number equivalence of a same position in different sequences (menu: Number trltor)
Input: list of accession numbers, window, reference
Output: absolute and relative position numbers according to the chosen alignment
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Go to page bottom Sequence viewer
Go to page bottom Display the sequence of catalytic domain (menu: Seq.viewer)
Input: accession number
Output: fragment of the sequence matching the accession number used in the alignment
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Sequence set maker

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1
Select a set from the whole displayed sequence list (menu: select)
Input: click checkbox in a list
Output: set of corresponding accession numbers to copy and paste
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2
Select a set from the whole hidden list by keywords (menu: keywords)
Input: keywords (name, organism ...)
Output: set of corresponding accession numbers to copy and paste
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3

Select a set of sequences close to a reference sequence (menu: close to)
Input: sequence name, level of identity or similarity.
Output: set of corresponding accession numbers to copy and paste

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4

Select a set of sequences from a motif (menu: motif)
Input: amino-acid sequence, level of identity or similarity.
Output: set of corresponding accession numbers to copy and paste

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5

Select a set of sequences with specified constraints (menu: filter)
Input: residu constraints
Output: set of corresponding accession numbers to copy and paste

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6
Perform logical operations on sets (menu: set operators)
Input: 2 sets of accession numbers, 1 operator
Output: new set of accession numbers to copy and paste
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7
Save and read sets localy (menu: Save/read sets)
Input: set of accession numbers
Output: set of accession numbers
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Sequence alignment

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1

Multialignment of sequences (menu: alig)
Input: set of accession numbers, method
Output: aligned amino acid sequences

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2

View a window in the sequence alignment (menu: window)
Input: Aligned sequence set, window limits
Output: Aligned sequence in the specified window in property-color-code

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3

Submit your sequence to Clustal W (menu: alig custom)
Input: set of accession numbers + your amino-acid sequence(s)
Output: aligned amino acid sequences

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Sequence analysis

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1

Display the distribution of amino acids at specified positions (menu: AA freq)
Input: set of accession numbers or residue constraints and list of positions to analyze
Output: amino-acid frequencies table

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2

Look for set-specific residues (menu: Specific)
Input: sets of accession numbers and operators
Output: list of residue positions, 1D, 2D and 3D-structure display

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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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