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The CGAT DataServer package is a collection of data construction scripts and CGI scripts. The data construction scripts run several programs to generate comparison data to be visualized by the AlignmentViewer program. AlignmentViewer can obtain data through the Internet using the CGI interface implemented in the server package. Alternatively, AlignmentViewer can also obtain data from the $CGAT_HOME directory when the server and client are installed on the same machine.
Data generated by CGAT DataServer can be classified into the following three classes:
A collection of locally aligned segment pairs between two genomes, which are displayed on both alignment and dotplot display panel in AlignmentViewer.
A collection of feature segments in each genome, which can be displayed on the feature segment tracks in AlignmentViewer.
A value associated with each gene, which can be used to assign color to that gene in AlignmentViewer.
Table 1. List of directories on the $CGAT_HOME directory
| Directory | Contents |
|---|---|
| database | The current release of the database, which is accessed by the CGAT CGI scripts |
| database.work | Space for constructing the new database release |
| work | Workspace for database construction where many intermediate files are generated. |
| perllib | Perl libraries. |
| etc | Configuration tables etc. |
| build | Scripts for constructing the database |
| commands | Commands for identifying several feature segments on each genome. |
| htdocs | HTML documents and CGI scripts |
| client | Java source code of the client program (AlignmentViewer) |
Table 2. List of directories on the database directory
| Directory | Contents |
|---|---|
| genomes | Genomic sequences |
| genes | Gene information, including position table (tab subdirectory), nucleotide sequences (nt subdirectory), and amino acid sequences (aa subdirectory) |
| alignment | Collection of genome alignments calculated by several programs |
| segments | Collection of feature segments calculated by several programs |
| geneattr | Collection of gene attribute values calculated by several programs |
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| Configuring AlignmentViewer | Database construction |