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Contents
Contents
The manual
Version 3.5
©1997-2021 Luc Moulinier and CSTB
Complex Systems and Translational Bioinformatics,
The ICube laboratory
Centre de Recherches Biomédicales de Strasbourg (CRBS)
1, rue Eugène Boeckel
67 000 Strasbourg
FRANCE
Contents
1
Obtaining and Installing
1
.
1
Requirements
2
Introduction
2
.
1
Context
2
.
2
Ordalie
3
Ordalie Basics
3
.
1
Alignments and sequences names
3
.
2
The Main Window
3
.
2
.
1
The Menus and the icons bar
3
.
2
.
2
The Snapshot bar
3
.
2
.
3
The Alignment Frame
3
.
2
.
3
.
1
Sequence names
3
.
2
.
3
.
2
Amino acid sequences
3
.
2
.
4
The Scores frame
3
.
2
.
5
The Control Panel
3
.
3
Features
3
.
4
Tools
3
.
5
Conventions
3
.
5
.
1
Mouse Buttons
3
.
5
.
2
Selections
3
.
5
.
2
.
1
Sequence names selections
3
.
5
.
2
.
2
Selecting a residue range
3
.
5
.
3
The database and the Ordalie file format
4
Sequence Tools
4
.
1
The Identity tool
4
.
1
.
1
Control panel
4
.
1
.
1
.
1
Selection
4
.
1
.
1
.
2
Computation and Results
4
.
2
The Search motif tool
4
.
2
.
1
The pattern syntax
4
.
2
.
1
.
1
Basic syntaxic rules
4
.
2
.
1
.
2
Implied Sets and Repeat Counts
4
.
2
.
1
.
3
OR Matching
4
.
2
.
1
.
4
NOT Matching
4
.
2
.
1
.
5
Begin and End Constraints
4
.
2
.
2
Control panel
4
.
3
Sequence information browser and editor
4
.
3
.
1
Browsing information
4
.
3
.
2
Editing information
4
.
4
VRP
4
.
4
.
1
The Drawing Area
4
.
4
.
2
The Control panel
4
.
5
Feature Editor
4
.
5
.
1
Control panel
4
.
5
.
2
Notation and Actions
4
.
5
.
3
Contextual Menu
4
.
5
.
3
.
1
Select Item
4
.
5
.
3
.
2
Select All Items
4
.
5
.
3
.
3
Select Region
4
.
5
.
3
.
4
Clear Selection
4
.
5
.
3
.
5
Edit Item
4
.
5
.
3
.
6
Define New ...
4
.
5
.
3
.
7
Delete selected Items
4
.
5
.
3
.
8
Propagate Items to this group
4
.
5
.
3
.
9
Propagate Items to All
5
Alignment Tools
5
.
1
Snapshot Overview
5
.
1
.
1
The snapshot frame
5
.
1
.
2
Control panel
5
.
2
Editor
5
.
2
.
1
Control panel
5
.
2
.
1
.
1
Clear
5
.
2
.
1
.
2
Group
5
.
2
.
1
.
3
Ungroup
5
.
2
.
1
.
4
Lock/Unlock
5
.
2
.
1
.
5
Rem. Col. Gap.
5
.
2
.
1
.
6
Temp. Save
5
.
2
.
1
.
7
Save & Return
5
.
2
.
1
.
8
Cancel
5
.
2
.
2
Edition actions
5
.
3
Clusters
5
.
3
.
1
Manual Clustering
5
.
3
.
2
Clustering Tool
5
.
3
.
3
Criterions
5
.
3
.
4
Algorithms
5
.
3
.
5
Control panel
5
.
3
.
5
.
1
Selections
5
.
3
.
5
.
2
Clustering criterions
5
.
3
.
5
.
3
Clustering methods
5
.
3
.
5
.
4
Other buttons
5
.
4
The Tree tool
5
.
4
.
1
Control panel for tree building
5
.
4
.
1
.
1
Selections
5
.
4
.
1
.
2
Options
5
.
4
.
1
.
3
Draw / Return
5
.
4
.
2
The Tree window
5
.
4
.
2
.
1
The Drawing area
5
.
4
.
2
.
2
The Control panel
5
.
5
The Conservation tool
5
.
5
.
1
Methods
5
.
5
.
1
.
1
The 'Threshold' method
5
.
5
.
1
.
2
The automatic methods.
5
.
5
.
2
The Control panel
5
.
6
Superposition tool
5
.
6
.
1
The superposition algorithm
5
.
6
.
2
Control panel
5
.
6
.
2
.
1
Selection
5
.
6
.
2
.
2
Control
5
.
6
.
3
Example : dealing with a homodimer.
5
.
6
.
3
.
1
Only one chain present in the snapshot
5
.
6
.
3
.
2
Moving a dimer.
5
.
7
3D Viewer
5
.
7
.
1
Molecules and Objects
5
.
7
.
2
Representation types
5
.
7
.
3
The 3D Viewer window
5
.
7
.
3
.
1
Quick Mapping
5
.
7
.
3
.
2
Molecular Objects frame
5
.
7
.
3
.
3
The 3D window
5
.
7
.
3
.
4
The Actions panel
5
.
7
.
4
The Object Editor
5
.
7
.
4
.
1
Making / Editing an object
5
.
7
.
4
.
2
Residue selection
5
.
8
The Features Summary
5
.
8
.
1
Drawing Area
5
.
8
.
2
Control panel
5
.
9
Barcode alignment
6
Menus Description
6
.
1
The File Menu
6
.
1
.
1
Open
6
.
1
.
2
Save
6
.
1
.
3
Save As ...
6
.
1
.
4
Save Window As
6
.
1
.
5
Close
6
.
1
.
6
Print
6
.
1
.
7
Quit Ordalie
6
.
2
The Edit Menu
6
.
2
.
1
Cut
6
.
2
.
2
Copy
6
.
2
.
3
Paste
6
.
2
.
4
Preferences
6
.
3
The View Menu
6
.
3
.
1
Bigger font
6
.
3
.
2
Smaller font
6
.
3
.
3
Open Log Console
6
.
3
.
4
Output Log as ...
6
.
3
.
5
Toggle FullScreen
6
.
3
.
6
Show/Hide Icon Bar
6
.
3
.
7
Show/Hide Scores
6
.
3
.
8
Show/Hide Features frame
6
.
4
The Sequence Menu
6
.
4
.
1
Names as
6
.
4
.
2
Identity tool
6
.
4
.
3
Search motif
6
.
4
.
4
Retrieve Seq. Info.
6
.
4
.
5
Browse Info seq
6
.
4
.
6
Edit Info Seq
6
.
4
.
7
Sequence VRP
6
.
4
.
8
Show/Hide Phylum
6
.
4
.
9
Show/Hide Sec. Str.
6
.
5
The Alignment Menu
6
.
5
.
1
Editor
6
.
5
.
2
Overview
6
.
5
.
3
Conservation
6
.
5
.
4
Tree
6
.
5
.
5
Features Summary
6
.
5
.
6
Features Editor
6
.
5
.
7
Annotate snapshot
6
.
5
.
8
Barcode
6
.
5
.
9
Clustering
6
.
5
.
10
Add separator
6
.
5
.
11
Remove Separator
6
.
5
.
12
Remove All separators
6
.
5
.
13
Toggle physicochem. col.
6
.
6
The Structure Menu
6
.
6
.
1
Superpose Structures
6
.
6
.
2
Display Structures
6
.
6
.
3
Color Sec. Str. by identity
6
.
6
.
4
Save PDB
6
.
7
The "?" Menu
6
.
7
.
1
About
6
.
8
help
7
Appendix
7
.
1
The command line options
7
.
2
The Ordalie database scheme
7
.
3
The Vector Norm scoring method
7
.
4
The Feature File Format
7
.
5
The superposition algorithm
Bibliography
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