Bindley Bioscience Center


Scientific and Educational Software: Clone Manager Professional Suite, Version 8

Software Initial Clone_Manager_Screen_Final

Clone Manager Screen Initial     Clone Manager Screen Final

The Clone Manager Professional Suite (version 8) provides a comprehensive set of tools for sequence manipulation and analysis, sequence alignment, and primer design. Researchers can also use Clone Manager as a quick and easy way to view or edit sequence files, find open reading frames, translate genes, or scan molecule files to search for genes or text. The molecule viewer window places all molecule information in one convenient location. Click tabs at the bottom of the window to see the molecule map, restriction map data, sequence, features table, or molecule information. Set the display style for the sequence data and select additional information to appear along with the sequence (like enzyme sites, sequence labels, or translation).

Clone Manager acts as an expert system to assist with cloning simulation, enzyme operations and graphic map drawing. Clone Manager will find restriction enzyme sites, cut molecules, modify ends, and ligate DNA. Through all of these operations, Clone Manager will track experiment features and enzyme sites, automatically renumbering positions in the new molecules. A very fast and powerful restriction enzyme analysis function will help researchers find enzymes for needed operations. View the resulting data in five different formats and filter the data to limit the display to only those enzymes of interest at the present time.

Graphic maps are drawn quickly and accurately.  High-resolution maps can be sent to a printer or to a Windows clipboard for use in another application. A map format option allows the addition of text information (description, notes, map features, enzyme sites) to a printed map page -- a great format for lab notebooks. Use the new Enhanced View of the graphic map to customize a special molecule map or a figure for use in a presentation or a publication. Adjust each individual feature's style, color, pattern or position; drag feature names with the mouse to position them exactly where wanted. Extra fonts, colors, styles and line width controls provide the ability to design very special maps.

Alignment Operations in the Clone Manager Suite can be used to perform multiple sequence alignments, local alignments and fast scans for sequence similarity. The program competently handles large numbers of molecules and large sequence sizes. Alignment results are displayed in a comprehensive tabbed-viewing window and results can be printed or copied to a Windows clipboard. A new module allows assembling sequences for simple or complex projects or for locating subclones on a reference sequence.

Primer Operations provides powerful search functions to find a 'short list' of optimal primers in target regions. A primer can be positioned in the molecule sequence at a target position.  The primer evaluation, the sequence flanking the primer, genes that are nearby, and the location of neighboring primers that will meet the criteria set can all be seen. A primer can be entered at the keyboard, analyzed, and linked to a molecule. Save primers to disk files or to a new collection of files; scan these files to search for binding sites for these primers on any molecule.


Purdue University
Bindley Bioscience Center
Integrated Screening Technologies
BIND-Room 222
1203 West State Street
West Lafayette, IN 47907-2057
(765) 496-2869

Larisa Avramova
Ph.D. Research Scientist