CoGeBlast Settings

This page contains a detailed list of CoGeBlast settings.

URL Parameters

The general URL parameters for CoGeBlast are as follows:

CoGeBlast.pl?param_name1=<parameter>&param2=<parameter>&param3=<parameter> etc.

URL parameters are used to load sequences into CoGeBlast. There are two methods of doing this: using Features, or using Datasets

Parameters Utilizing Features

General form:

CoGeBlast.pl?fid=1234&fid=5678&fid=...&rc=0&gstid=3

• fid

This is a list of feature ids that instruct CoGeBlast to load sequences associated with the features the feature ids represent. An example is below:

CoGeBlast.pl?fid=1234&fid=5678

The above ... indicates that any number of fids may be strung together in the URL.

Note: No numbering is associated with the "fid" - i.e the parameter list

CoGeBlast.pl?fid1=1234&fid2=5678

is incorrect and will result in sequences not being properly loaded.

Parameters Utilizing Datasets

General form:

CoGeBlast.pl?chr=3&upstream=4562&downstream=9042&rc=0&gstid=3

• dsid

This is a dataset id for the sequence to be loaded.

• chr

This is the chromosome from the dataset associated with the dataset id.

• upstream

This represents the start position of the sequence on the chromosome selected.

• downstream

This represents the stop position of the sequence on the chromosome selected.

Parameters Utilized In General

• rc

Select whether or not to reverse complement the sequence(s) being entered into CoGeBlast. Boolean value, with 0 being no reverse complementation, and 1 being yes.

• gstid

'TODO'