Sci-Ed Software
Software for the Molecular Biologist

New in Clone Manager Professional 9

New Features

New Sequence Phrase Collections -- You can now construct and use collections of sequence phrases. You can use these collections to find sequence phrase sites in a specific molecule, requiring an exact match or permitting limited mismatches. You can also scan for molecules that contain a specific sequence phrase.

New Gateway® Cloning Wizard -- Use the new Gateway Cloning Wizard to simulate cloning using Gateway® Recombination Cloning techniques (Invitrogen Corp). It will help you select the appropriate components, show you the proposed result, and create the resulting recombinant molecule. If you are using a Multisite Pro kit, the wizard will walk you through constructing multiple fragments with the right attB sites and donor vectors.

New Topoisomerase Cloning Wizard -- Use the new Topoisomerase Cloning Wizard to simulate cloning using Topo® Cloning techniques (Invitrogen Corp). It will help you select the appropriate components, show you the proposed result, and create the resulting recombinant molecule.

New Assembly Cloning Wizard -- Use the new Assembly Cloning Wizard to simulate cloning using Gibson Assembly™ (Synthetic Genomics, Inc.) or related cloning techniques. It will help you select the appropriate components, show you the proposed result, and create the resulting recombinant molecule.

New Retrieve from Entrez (E-utils) -- You can now retrieve sequence files from the Entrez system at NCBI using a new module based on E-utils that can directly access the NCBI file system (instead of using the Entrez web site browser interface). Once you locate the file you need, you can view the file in GenBank format or import the molecule for immediate use in Clone Manager.

New support for GenBank joins, qualifiers -- You can now read in segmented features (joins) when importing GenBank files and you can enter join segments for your own sequence files, as needed. Clone Manager also can now read in, display, and retain feature qualifiers for imported GenBank files. Use a new features table toolbar button or a special mouse cursor to view this information.

New support for translation tables (genetic codes) and codon start settings -- You can now specify the codon start (offset for the first complete codon) of a feature that can be translated and this information can be read in when importing GenBank files containing this qualifier. You can also set the translation table (genetic code) to be used for translation for your molecule and this information can be read in for features when importing GenBank files containing this qualifier. Translation table and codon start settings will be used by functions that translate relevant sequence data.

New Sequencing Primer Wizard -- Use the new Sequencing Primer Wizard to design a set of primers for sequencing a molecule region. Specify primer type, optimal primer length, preferred primer spacing. Export primer sequences or create a new primer collection in one easy step.

New Join Sequences function -- Use the new Join Sequences function to join two sequences to create a larger molecule. You can select to append, splice, or insert one sequence to another. Molecule features (genes, regions, etc) will be retained and enzyme sites for the new molecule can be auto-scanned anew or rebuilt from existing site lists.

New PCR Cloning Wizard -- Use the new PCR Cloning Wizard to design PCR primers to amplify the region of a molecule you want to clone, use enzymes to prepare the vector or the region for insertion, and then generate recombinant molecules. You can view several solutions and save selected primers, amplified products, and recombinants for later use.


Updated GenBank feature keys and qualifiers -- The Clone Manager list of feature keys supported in GenBank / EMBL file formats has been updated to include new feature keys (like Regulatory) and mandatory qualifiers are now supported. You can modify your list of designated feature keys that should be imported when you open a file in standard GenBank or EMBL format using File, Preferences, Import Features.

Updated File, Open and File, Save dialog boxes -- Clone Manager now uses the updated Windows File, Open and File, Save dialog boxes. These dialogs are complete with a navigation pane, search box, choice of views and an Organize menu. The custom buttons Work Boxes, Add Work Box, CM Home, and Paste Molecule have been eliminated, but their functions can be achieved using alternative procedures (see FAQs section for more details).

Updated application Help -- the application Help has been updated to eliminate the use of ActiveX and related controls. Context-sensitive help is no longer provided, but you can navigate to all topics using expanded menus. For specific help questions, a simplified Search pane lets you enter keywords and find related topics.

Improved on-screen Working Map -- New anti-aliasing (smoothing) of feature and map lines on screen improves the appearance of the working map. New color segment shown on map when a feature is selected -- helpful in marking the feature extent close to the map line, where enzyme or primer sites are positioned. New mouse hover setting lets you move mouse to a site to show basepair position (no click required). User can enable or disable these new options in Format Map, Screen Basics.

Updated Map Sites List -- The scrolling map sites list (right side of Map display) now shows enzyme sites, primer sites (Professional edition), and features. Click on site list header control to select what the list displays. Click on column headers to sort. Enzyme site information now includes the type of ends produced (5' sticky, 3' sticky, blunt) and an indication if this enzyme is a single cutter (sc), cutting this molecule only once. Use toolbar buttons to begin actions with enzymes, primers or features selected on map sites list.

New Enzyme List Interface -- New, easier-to-use enzyme list display. Additional information shown for each enzyme, including bases in overhang. Easier access to enzyme information (suppliers, isoschizomers, etc). New ability to sort enzyme list on any information, including enzyme recognition sequence.

Create Fragment from feature -- You can use a new toolbar button on the Features tab in the molecule viewer window to prepare a new molecule from the fragment of sequence containing the selected feature. You can include extra bases at each end of the feature sequence and, if the feature is on the complement strand, you can choose the orientation of the new molecule.

Export Feature Sequence -- You can now select a feature in the feature table display and use the new toolbar button Export Sequence to export the sequence of the feature to a disk file or copy the sequence to the Windows clipboard for use in another program.

Jump to Formatted Sequence -- From the molecule map or features table, you can use new GoTo toolbar buttons to jump to the formatted sequence display at the position of an enzyme or primer site, or at the start or end of a feature. Within the sequence display, use the GoTo button to quickly move to the part of the sequence containing the basepair position number entered.

Easier Enhanced View Export -- You can use the new Copy/Export View button to send your enhanced view map to the Windows clipboard or to a disk file in vector or raster (bitmap) file formats. Select low-res or high-res output. Improved raster output (tif, png, gif) with line smoothing for features and map lines.

Updated, easier-to-use DataBook database -- New DataBook user interface, new xml databook file format. Create new databook files and create folders to organize your databook files. Updated Search function to find files with genes or text strings and list in a new Search Results folder. Share databooks as read-only resources (multi-user licenses).

Create new DataBooks with batch operation -- Use the updated Multiple File Converter to create new databooks from existing molecule or data files in one easy batch operation. Create one new DataBook table for all the molecule files in one folder or make a separate databook table (file) for each folder of files found in the specified location.

New DataBook Tools -- If you have moved your molecule files from one location to another or have changed a mapped drive letter or renamed folders, you can use new DataBook Tools to quickly and easily do a find and replace operation on the file name field in a selected databook. You can also use DataBook Tools to convert old databooks into the new format.

New Color Setting for Highlight bars -- You can now assign the highlighter color to be used to mark the selected (highlighted) item in results screens like the Restriction Map or Analyze Molecule displays if the default color does not show up with sufficient contrast on your display. The Highlighter Color (File, Preferences) is used to highlight objects or draw marker lines and you can change this color to improve visibility, as needed.

Multiple Sequence Alignments with filenames -- Molecules selected for multiple sequence alignments can display the molecule name or file name, up to a maximum of 16 characters. If the name is too long, the program will truncate the name, using the rule you select. Use the Name settings button in the alignment setup dialog box or Align, Alignment Parameters and Settings, Name Settings to set your preferences.

Store Name, Description for alignment results -- You can now enter descriptive information about an alignment or assembly. When you save the results to disk, this information will also be saved. If you use the Add to DataBook function, the descriptive information will automatically be added to the databook record. You can view or modify this descriptive information using the new toolbar button Edit Name in the alignment or assembly results window.

Save Modified Trace Files -- When viewing sequence assembly or alignment results, you can recall a base in a trace file if you believe there is an error. You can now elect to update the sequence in that trace file and overwrite the file on disk.

Change Name of Molecule in alignment results -- You can change the name of an aligned molecule when you are viewing the alignment results or when you are setting up an alignment. Just right-click on the molecule name in the results display, and then enter the new name for the aligned molecule. During setup, use the Edit Item button in the setup dialog box and edit the Name to Display.

Find Sequence update -- You can now find places in the sequence that nearly match a specific pattern of bases. The updated Find Sequence module now has options to allow limited mismatches or mismatches and gaps or insertions when comparing the molecule sequence to the specified search sequence. Create a molecule feature from a found site in the scrolling report of all sites found.

Save Compare Two Sequences results -- You can now save the results of a Compare Two Sequences alignment operation and later re-open this results file and continue to review the data. All alignment results data can now be saved to disk files and special extensions are used to identify these files.

Substyles for Gene, Region, Marker types -- Feature Draw as Types (Genes, Regions, Markers) are used to tell Clone Manager how to display a feature on the molecule map or annotated sequence. You can now have three different styles within each of the major feature drawing types. These styles can be set using map format options and can be specified as part of the import filter for GenBank files.

Updated Clone Manager XML format -- XML files (*.cx5) prepared by Clone Manager 9.2 and later are encoded UTF-8 to add support for international characters. The updated xml file format can also contain feature qualifiers and nested features to hold feature segments (joins). (The xml format is often used for data exchange.)

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