5.2 Configuring qodgui

Opening the Preferences from menu allows you to configure . It has three items: Genomes, Alignments, General.

General (see fig:qod:config-grlTab) enables you to choose the language used in between the system default language, French, or English. This tab allows to enable/disable cache usage for storing available central genomes and pairwise comparisons. If cache is enabled, then you can set the update frequency. This feature has been introduced in version 0.8.0, in order to reduce the loading time when the number of available central genomes and comparisons becomes important.

Figure 5.3: Screenshot of the General tab of the preference dialog.

With Genomes (see fig:qod:config-genTab) and Alignments (see fig:qod:config-alnTab) you can set the parameters regarding the parts of the input that are respectively, genomes and theirs annotations, or the files containing the local alignments for a center and a compared genome. For each, they should be located under a "genome", resp. an "alignments", directory. This directory can, should, be organised as a tree of subdirectories, one for each central genome. will look for input files until a user specified recursion depth.

For the central genomes, we choose

• the extension of the sequence files (fasta formatted files),
• the extension of the annotation files,
• whether you want to load the annotations if a file is available for your center
• whether it should display in the selection window only the genomes for which some alignments are available, i.e., those on which qod can run.

Figure 5.4: Screenshot of the Genome tab of the preference dialog.

For the pairwise comparisons of genomes, we choose

• the extension of the alignment files between .axt, .mat, .txt, or .res files,
• the alignment separator symbol.

Figure 5.5: Screenshot of the Alignment tab of the preference dialog.

Suppose that your create a directory (say D:\QOD_Data under windows, $HOME/QOD_Data under Linux/Macos). You should create two subdirectories names (for example) Genomes and Alignments. For each central (e.g., genome AP009048 of Escherichia coli), create a subdirectory having the same name (e.g., Escherichia_coli) under Genomes and Alignments. Copy the data files of under each corresponding subdirectory. For the given example, let us suppose that you have three fasta files for the central genome and compared genomes, say AP009048.fas, CP000243fas and CP000247.fas. You compute the pairwise local similarities between AP009048.fas and CP000243fas and AP009048.fas between CP000247.fas (see External Resources). You store them following the mat format (see Invoking qod and qodgui) or the axt format into files named AP009048_CP000243.mat and AP009048_CP000247.mat (set .axt extension if you use axt format). It is recommended to compress all your files using gzip for reduce your disk usage. Then move the .fas[.gz] files into D:\QOD_Ddata\Genomes\Escherichia_coli (windows) or $HOME/QOD_Data/Genomes/Escherichia_coli (Linux/Macos). If you have annotations for your central genome, name the file with the same basename and move it in the same directory as the fasta files (e.g., D:\QOD_Ddata\Genomes\Escherichia_coli\AP009048.tbl[.gz] under windows or $HOME/QOD_Data/Genomes/Escherichia_coli/AP009048.tbl[.gz] under Linux/Macos). Move the .mat[.gz] (or .axt[.gz]) files into D:\QOD_Ddata\Alignments\Escherichia_coli (windows) or $HOME/QOD_Data/Alignments/Escherichia_coli (Linux/Macos).

Now, go to the Edit menu, then select Preferences (Macos users won't find this item in the menu but located in the Macos usual place). In the Genome tab, set the genome directory to D:\QOD_Ddata\Genomes (windows) or $HOME/QOD_Data/Genomes (Linux/Macos) and the extension to .fas. In the Alignments tab, set the alignment directory to D:\QOD_Ddata\Alignments (windows) or $HOME/QOD_Data/Alignments (Linux/Macos) and the extension to .mat (or .axt) and the separator to _. Click the Ok button, a dialog box may ask you to return to the first screen, answer yes. Now, you can select the available central genomes and see what alignments are available with it. Select at least one of them and click Ok.

All extensions can be followed with a ".gz" meaning that the corresponding files can be compressed with gzip. will automatically uncompressed them when needed; it is totally transparent to the user.