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?dsid=51223&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'