The CGAT DataServer package

Overview of CGAT DataServer

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.

Feature Segments

A collection of feature segments in each genome, which can be displayed on the feature segment tracks in AlignmentViewer.

Gene Attribute

A value associated with each gene, which can be used to assign color to that gene in AlignmentViewer.

Directory structure

Table 1. List of directories on the $CGAT_HOME directory

databaseThe current release of the database, which is accessed by the CGAT CGI scripts
database.workSpace for constructing the new database release
workWorkspace for database construction where many intermediate files are generated.
perllibPerl libraries.
etcConfiguration tables etc.
buildScripts for constructing the database
commandsCommands for identifying several feature segments on each genome.
htdocsHTML documents and CGI scripts
clientJava source code of the client program (AlignmentViewer)

Table 2. List of directories on the database directory

genomesGenomic sequences
genesGene 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