Multiple Cloning Sites

There is a special class of annotation for Multiple Cloning Sites.

To activate, select the 'MCS' check box in the 'annotation' creator/Editor or use 'Multiple Cloning Site' as a catagory for a 'Vector Feature'

Restriction sites present within an 'MCS' annotation can be displayed in a special way on the linear 'Map' and 'Circular Map' displays

linear 'map' with 'MCS Only' check box selected

circular 'map' with 'separate' check box selected in the MCS section of the 'Enzymes' panel


Restriction enzyme sites are included in 'MCS' displays if they are present only within set 'MCS' annotations or features sequences. eg if an MCS sequence contains two BamH1 sites, both will be displayed. However, if an MCS contains a BamH1 site, and sequence outside set MCS locations also contains a BamH1 site, the MCS display will not contain the BamH1 site, as it would not be useful for cloning.