GET protocol

The GET protocol will retrieve data from a web server using the HTTP-GET protocol.
The protocol has two configurable settings: Base URL and Parameters. The Base URL should point to a CGI-script running on a web server that can return track data for a given track and genomic sequence segment. Some CGI-scripts will only serve data for a single fixed type of track (e.g. DNA or RepeatMasker regions) and a specific genome build. Other scripts may be configured to serve data for different track types and different genome builds, and the requested track and genome build are then normally specified as part of the Parameters setting.

When MotifLab contacts the HTTP server, the value of the Parameters setting will be passed on as a query string (hence, the complete URL used will be: <Base URL>?<Parameters> ). The Parameters setting will thus have to be set according to the requirements of the particular CGI-script. However, all CGI-scripts must be able able to recognize three parameters that specify respectively a chromosome, a start coordinate and an end coordinate of a genomic segment and the script should then only return data for this segment (start- and end-coordinates assume the chromosome starts at position 1 not 0). The three placeholder variables $CHROMOSOME, $START and $END must be included as part of the Parameters, and these placeholders will be replaced by an actual chromosome name, start coordinate and end coordinate when MotifLab contacts the server to obtain data for a sequence.