Subsections
5 Menus Description
This chapter describes all the Ordalie menus. Only the entries which have not been already explained in this manual will be described in details here.
Opens an alignment file. Several file formats are recognized:
- TFA (Fasta) file format.
- MSF (Multiple Sequence File, GCG Wisconsin Package) format.
- Macsim/XML format. The Macsim format is an XML file output of the MACSIMS program or server (see [15] and http://www.lbgi.fr/ julie/MACSIMS/ for details).
- ALN (ClustalW) file format [14].
- RSF file format (Rich Sequence File), as output by the SeqLab program [16].
- ORD (Ordalie) file (ORD), Ordalie specific file format.
A format checking is done using the file extension (. tfa/. fasta, .msf, .xml, .rsf, .aln or. ord recognized) against the file content. In case of inconsistency, the user will be asked for the correct file format.
Save the entire current snapshot in the current file format with the current file name. The first time 'Save' is invoked, the user will be prompted to enter a file name. Subsequent call too “Save” will save the snapshot using the defined name and file format.
Ask for a file format and a file name to save the current snapshot. If there are selected sequences, the user is asked to save all sequences or the selected ones.
Save only the visible part of the snapshot in the specified file format and file name.
Close all snapshots and all dependencies (Overview, 3D Viewer... ), and set Ordalie ready to load a new file.
When the 'Print' option is invoked, a 'Setup' properties window will pop up. Several printing parameters can be set:
- image format : actual choices are PostScript, JPEG and PNG.
- Paper size : A4, A3 or US letter.
- Paper orientation : Landscape or Portrait
- Font size and weight : the font used to print alignments is always Courier New. By default, the font size is the same as the one used in the main Ordalie window. It can be changed from 6 to 14 by steps of 2 pts, adn the weight of the font can be 'normal' or 'bold',
- Print Area : By default, the whole alignment is printed. It is possible to print only the current window or the selected sequences can be printed too.
- Ruler : if desired, a ruler can be printed at the bottom of every page.
- Residue numbering : if desired, the residue numbering inside the sequence can be printed on every page for every sequences.
Guess...
Cut the selected sequences.
Copy the selected sequences into the memory buffer.
Paste the sequences present in the memory buffer. The sequences are pasted just below the current selected sequence. If no sequence is selected, then no sequences are pasted. Note that in case of pasting sequences that already exist in the snapshot, their names will be suffixed by '__<n>' where '<n>' is the copy number.
Access the 'Preferences' panel. This gives access to Ordalie internals.
Increases the font size for sequence display. The Ordalie default font type and size can be defined through 'Edit' -> 'Preferences' -> 'General'.
Decreases the font size for sequence display.
Most of Ordalie information and computations are logged. The Log window allows accessing the crude log text and to save it as a raw text file.
This will output the whole Ordalie lo in a file. A cascade menu allows selecting between an HTML or Text format. The output file name is the root name of the original alignment file suffixed by the format type.
Toggles the main window between its actual size and full screen size. This can also be achieved by hitting the <F1> key on the keyboard.
Displays or hides the Icon bar buttons frame. This is useful when a maximal window size is required, for alignment editing for example.
This turns on and off the scores frame. When displaying a conservation score, either through the Features buttons or inside the 'Conservation' tool, the global score and groups scores for each column is plotted. By default, the Score frame is turned off.
This turns on and off the Features frame. This is useful when a maximal window size is required, for alignment editing for example.
If the “life domain” characteristic information is available for the sequences, then the sequence names are coloured according to their life domain : eukaryots in red, archaea in blue, bacteria in yellow, and viruses in black.
Colours the sequences according to their groups.
If the secondary structures are available, show or hide -helices (red) and -strands (green).
In Ordalie, there are several ways to display sequences names:
- by the sequence name, which is a name given by the user,
- by the accession number,
- by the bank Id,
- by the full organism name if available,
- by the Gene.Species abbreviation if available. The abbreviated names are of the form Homo.sapi for Homo sapiens, sacc.cere for Saccharomyces cerevisiae for example.
By default, the Sequence Name is displayed.
In Macsims/Xml and Ordalie file formats, the Sequence Name, Accession Number and Bank ID are clearly identified for each sequence. For all other formats, there is only one ID per sequence, and this one will be taken as the sequence name, accession number and bank ID.
Launches the Identity tool, see 4.3.
Launches the Search motif tool, see 4.4.
5.4.4 Retrieve Seq. Info.
This command is intended to retrieve information for some sequences by querying their original databases. When invoked a window appears asking if all sequences or only the selected ones should be treated. After pressing “OK” Ordalie will query the database to which the sequences belong to and retrieve corresponding information. If some amino acid sequences have changed, they will be immediately realigned against the other sequences with the MAFFT program. Once terminated a summary window appears showing the number of updates that occurred for Accession, Phylum, Taxa ID, Organism, Description and the amino acid sequence. Below the changes table the “Show details...” button launches a web page with the detailed changes that occurred for each sequence.
5.4.5 Edit Info Seq
Enters the sequence information edit tool. This tool gives access to all information available for a given sequence, and allows modifying some of them.
At the top of the “Edit Info. Seq.” window a combobox allows selecting the desired sequence.
Launches the Features Editor tool, see 4.10.
Opens a file dialogue asking for a feature file. The loaded features are immediately available in Ordalie. The feature file format is described in Appendix 6.4.
Launches the Feature Summary tool, see 4.11
This item triggers a menu allowing to add sequences or PDB from files or database. Choices are:
- Sequences from database: download sequences from UniProt/RefSeq databases given the user specified accession list.
- Sequences from file: user supplied sequence file.
- PDB from sequence file:
- PDB from PDB ID: download a user supplied PDB ID.
Depending on the choice a dedicated window pops up with corresponding fields to be filled. Figure 17 shows the window for adding sequences from file.
Figure 17:
The window corresponding to adding sequences from file
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After specifying a file, PDB ID or accession numbers, the user should select whether:
- The added sequences should be aligned or not. Ordalie uses MAFFT to align the sequences against the snapshot sequences.
- To discard or to create a copy if there are duplicated sequences.
- To insert the newly added sequences at the bottom of the snapshot, just after a given sequence chosen by the dedicated combobox, or inserted into their corresponding cluster based upon sequence identity (only valid if added sequences are aligned).
After sequences have been added, features positions are recomputed if needed, and basics sequences characteristics are computed for the new sequences (isoelectric point, molecular weight, identity, composition, ...) and are logged.
Launches the Editor tool, see 4.2.
Re-aligns the selected sequences by using the MAFFT program [7,6,5,8]. The selected sequences are first degapped and then re-aligned against the remaining sequences. The re-aligned sequences stay at their original place.
Launches the Clustering tool, see 4.5.
In Ordalie a “separator” is simply a blank line between sequences. Adding separator allow the user to create his own clusters. This command will add a blank line separator just below the selected sequence. Be aware that only one sequence should be selected.
Removes the separator just below the selected sequence. Be aware that only one sequence should be selected.
Removes all separators, and unselects all sequences. This results in an unclustered snapshot.
Creates an instance of the Overview Window for the current snapshot, see “Snapshot Overview” section 4.1.
Launches Conservation computation tool, see 4.7.
Launches the Tree tool, see 4.6.
Launches the Annotation tool, see 4.12.
Launches the Barcode tool, see 4.13.
Launches the feature editor, see 4.10.
Launches the 'Features Summary' tool, see 4.11. Sequences selected in the main window will automatically be selected in the 'Features Summary' tool.
Toggle the colouring of residues with the same mapping as in the 'Editor'.
Launches the 'Superposition' tool if several PDB structures are available in the snapshot, see 4.8.
Launches the '3D Viewer' tool, see 4.9.
This tool allows colouring the secondary structures according to their sequence identity level in the snapshot. When invoked, a parameter window will pop up with the following parameters to select:
- Compute similarities using mean sec. str. limits or by using a sequence reference,
- Type of color gradient : grey or color,
- Gradient limits : from min to max identity, or from 0 to 100%,
- Assign identity to B factor or not.
As the 3D structures may be changed using the 'Superposition' tool, this option allows saving a given 3D structure present in the snapshot. It may be useful to output the superposed structures in order to render them in a more sophisticated drawing program.
When invoked, a window will pop up to ask the user for some parameters:
- select the molecule,
- select all or a particular chain,
- select all residues or a specific residue range,
This menu item pops up a window giving some information about Ordalie, such as the currently used version, and the URL for the Ordalie home page.
Launches this manual on the default web browser using local version.
Launches the Ordalie documentation on a web browser using Ordalie website.
