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Sci Ed Software
Software for the Molecular Biologist

New in Clone Manager 10

Clone Manager 10 is now DPI-aware and can take advantage of your high-resolution screen display. This means clearer text and better map drawing. In addition, new fonts are being used and a new color palette has been implemented. To accommodate those with smaller displays (smaller laptops and 2-in1’s in tablet mode), menus are now shorter, toolbars are shorter, and individual toolbar buttons are larger.

New Licensing Flexibility

With Clone Manager 10, the Individual User license and Small WorkGroup license classifications have been replaced with a simple Seat License configuration. Each seat license is installed on a single computer. You can order as many seat licenses as you need, with volume discount pricing applied to your order.

Each license is managed on its own computer -- you can activate a license, transfer it to another computer, or join a concurrent user group (if you are using the network concurrent version). The new License Management wizard will assist you with these tasks.

Concurrent-user license management is also easier and more flexible with Clone Manager 10. Installation of the licensing service on your network server can be as simple as possible, or you can use more advanced options to configure multiple licenses or multiple user groups. There is also a new, smaller license available (2-user concurrent license) and a fully functional time-limited evaluation license that will allow you to fully test how the concurrent license will perform in your environment.

Main toolbar, menu changes

The new main toolbar has some familiar buttons, some new buttons, and some buttons that have been removed and the functions accessed through the appropriate menu (Clone, Primer or Align).

A new toolbar section gives easy access to places you may want to visit often:

      toolbar

    Molecule List View list of loaded or newly-created molecules
    Primer List View active/loaded primers and primer collections
    Enzyme Lists View lists of enzymes or create new user lists
    Sequence Phrases View or manage your sequence phrase collection
    Data Book Simple built-in database for molecule information
    Add Entry Add an entry to DataBook or to a primer collection

Find in Files  New easy main toolbar access to Find in Files option. Use this to scan molecule files to look for certain genes or specific text in the molecule name or description, or search the Notes field in Clone Manager files (*.cm5).

Ligation Update

The ligation module now supports joining together two or more pieces of DNA. The new ligate display window shows you the molecules or fragments as they are being prepared for ligation.

In the upper half of the new window, an icon map of the active molecule is shown, with features (if any). If enzymes were used to create the molecule’s ends, these enzyme names appear above the respective end. The actual sequence of each end is shown below the map. The molecule in this window can be modified (see below). Use the Fragment Information button to view the features table for this molecule or to find enzymes that could prepare ends that would be compatible to the fragment to the left or right (in lower window).

In the lower half of the window, all of the molecules or fragments are shown in boxes. Click the Add Molecule button to select additional molecules to add to this window. You should arrange these molecules in the order in which they should be joined. Click on a molecule and drag to move to the right or left, as needed. Small icons appear between each fragment box to indicate if ligation is possible. If changes are needed to a fragment, click to select the fragment, causing it to appear in the upper box, where modifications can be made.

Use the Cut Fragment button to access the cut molecule operations for the selected molecule. You can cut a circular molecule to make it linear, cut out a region to be cloned, or cut with an enzyme to make a compatible end. Use the Modify Ends button to access the modify ends operations for the selected molecule. You can use standard or custom end modifications to prepare molecule ends for ligation. Use the Invert Fragment button to reverse (invert) the sequence of the selected molecule. Use the Undo button to undo the last modification to the selected molecule.

Ligate   Click the Ligate button to join all compatible ends of the fragments in the order shown. If you do not want the ligate operation to circularize the molecule, click on the drop-down arrow to the right on the Ligate button and select Do not circularize. Once ligation is complete, you can enter the molecule to the molecule list for further use or save it to disk.

New Cloning Wizards Implemented

The assembly cloning wizards now support Gibson Assembly, In-Fusion cloning and Ligation-Independent cloning techniques. The wizards will help you to select the appropriate components, show you the proposed result, and create the resulting recombinant molecule. Select one of the assembly cloning wizards from the Clone menu to get started.

Use the Ligation-Independent Cloning wizard to join fragments previously prepared with correct overlaps. Use the Gibson Cloning or In-Fusion cloning wizards to use PCR to create amplified fragments with overlaps, and then assemble the fragments, using the assembly procedure selected. Set the procedure and primer design options, if applicable.

Create Molecule  Click the Create Molecule button to have the program automatically do the required steps to simulate the cloning experiment, produce the recombinant molecule, and enter to the Molecule List.

Working Map Update

Working (on-screen) maps now show features in the style and color selected. Features with joins use a narrow line to connect the joined segments. The updated color palette produces well-balanced map figures in contemporary colors. Updated fonts improve feature name and enzyme site text.

Easy, right-click access to customization now includes the ability to select your three default styles. New toolbar button in map window to create an Enhanced View map.

Features Table Update

New user settings support displaying feature basepair positions as left-to-right or start-to-end. And you can now elect to show an iconic map of the molecule with selected feature highlighted above the table, and the selected feature map style/color and sequence color below the table.

The option to show information-only features on the features table is now included in Settings. New custom settings dialog box for features makes it easy to use the three default styles, as well as the individual feature custom settings. You may find it helpful to use style 1 (solids) for important features, and style 2 (shaded) or style 3 (open) for less-important features.

Molecule List Update

The molecule list now has the ability to show more information about the selected molecule. You can see the number of features, primers and enhanced maps contained within the molecule file, as well as the start of the Notes field. Use the More Info/Less Info button to show or hide this information.

BLAST Update

You can now set up a remote search using the NCBI BLAST server with the new Align, BLAST Search (NCBI REST) option. Results are displayed in a new table format. (If you prefer, you can still use the legacy WebBlast (NCBI Browser) option to perform the BLAST search using the built-in web browser to show the NCBI results data). With either results view, you can click the Get Molecule button to import the molecule directly into Clone Manager for use now.