Sci Ed Software
Software for the Molecular Biologist

Frequently Asked Questions

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General Topics

File Handling

Help File


Does Clone Manager work with Windows 10?

Clone Manager 10 and the last version of Clone Manager 9 (version 9.51) fully supports and is fully tested on the Windows 10, Windows 8, and Windows 7 operating systems. If you are still using Clone Manager 9, you can download a free incremental update to bring your software to version 9.51.

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Does my Clone Manager license expire on a specific date?

No, your Clone Manager license does not expire. You can continue to use your Clone Manager software for as long as it is useful to you. Technical support is available by email or telephone without additional cost.

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Access to the NCBI web site seems to have stopped working. What can I do to continue to use Clone Manager with Entrez or BLAST?

NCBI has changed the URL used to reach the web site (going to a more secure https link) and is phasing out the use of sequence GIs as sequence identifiers.

Clone Manager 10 and the last update to Clone Manager 9 (version 9.51) has the changes necessary to allow you to continue to use the Retrieve from Entrez (E-utils), Browse Entrez and Search, and BLAST internet search functions. If you are still using Clone Manager 9, you can download a software patch that will update your program to version 9.51.

If you are using earlier versions of Clone Manager, you can use the Entrez web site directly to find molecules of interest. Download molecules files to your computer in GenBank format and then later open the files with Clone Manager for further use.

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How can I paste a molecule into the new version of Clone Manager?

On the File menu, click Other Tools, Import from Clipboard to paste molecule data into a new molecule structure in the Clone Manager program.

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How can I copy my sequence to the clipboard in FASTA format?

With the molecule open in the molecule viewer window, click Tools, Export, Export Molecule Data. Set the option to FASTA in the upper section and set the option to Copy to the Clipboard in the lower section. Click OK. Your sequence data is now on the clipboard in FASTA format, ready to paste into another application. FASTA is a very simple format that is the required format for many sequence analysis programs, especially over the web.

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What's the easiest way to prepare a group of files to share with others?

You can use the multiple file conversion utility to convert a batch of files in Clone Manager format into the standard GenBank format, all in one easy step. Click File, Other Tools, Multiple File Conversion to get started. You can identify the files or folders of files to convert and specify the location (folder) where you want the program to save the files, and you can select the format to convert to. Files converted to the Compact GenBank format will contain essential molecule data in a format that is consistent with the standard GenBank file format and can be shared with others who do not use the Clone Manager program.

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How can I read in more/different features when importing a GenBank file?

If you are using a recent version of Clone Manager, you can identify the feature keys that should be imported when you open a file in standard GenBank or EMBL format. Just click File, Preferences, then the Import Features tab. Click the Add button to include a new feature key on the import list and select the Draw As feature type to tell the program how to display this feature in Clone Manager. (Note: complex features consisting of joins not supported in versions earlier than 9.2.)

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Can Clone Manager read in GenBank features with joins?

The latest versions of Clone Manager (ver 9.2 or later) adds support for GenBank joins (segmented features). If you routinely retrieve GenBank files that contain joins, you will want to change your import filter at this time. (If you do not change the import filter settings, Clone Manager will read in the CDS features with joins as well as the exons for each feature, resulting in maps with apparent duplicate features.) To change your import filter, click File, Preferences, Import Features. Select the feature key Exon, click the Edit button, and change the Draw As style from Gene to Info only.

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How can I see the basepair positions for join segments?

When viewing the Features display in the molecule viewer window, you can move the mouse over the small symbol to the left of the feature name. The cursor charges to a rectangle shape and you can click with this cursor to open a popup box that shows the location (basepair positions) for the feature segments and feature qualifiers. Click outside the popup box to dismiss. When viewing the Map, click on the feature to select (yellow highlight shows extent of feature) and then click the Properties toolbar button to see the join basepair position information. Click on any enzyme site to reset the right panel to the enzyme site list.

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My GenBank file has features with the Regulatory key. How can I read these into Clone Manager?

Clone Manager has a list of feature keys supported in GenBank/EMBL file formats and support for mandatory qualifiers. You can modify your list of feature keys that should be imported when you open a file in standard GenBank or EMBL format. Click File, Preferences, then click the Import Features tab. Click the Add button to include a new feature key in the designated features list. When the dialog box appears, select the Regulatory key from the list. Then select the Draw as Type to tell the program how to display this feature in Clone Manager.

If you select Region as the Draw as Type for Regulatory features, you will be able to see the features on your map and on the features table. You can later change small regulatory features to Labels or less important ones to Info Only if your map becomes cluttered. To change the drawing style for an individual feature, select the feature on the Features tab and click the Edit toolbar button.

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How do I use the Clone Manager Help system?

Click on the main toolbar Help button (far right) to open the Help system. Click on a category in the list provided to navigate to information within that category. For more specific help questions, click the Show button in the Help window toolbar to open the search pane on the left. Type in a keyword related to the help needed and click the List topics button. Then select the topic to display and click the Display button. Click the Hide button to close the search pane.

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I just downloaded a new Clone Manager help file and it doesn't seem to be working. What do I need to do?

Windows security updates can enable a block that will prevent the display of compiled help (*.chm) files you download from the internet. You may need to unblock this help file before use. In Windows Explorer, right-click on the Clone Manager help file you just downloaded and select Properties from the menu. Click the Unblock button (lower right) on the General page and then click Apply. If you do not see the Unblock button, you may need to log on as administrator.

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I'm getting an error message when I try to access Help in the network version of Clone Manager. How can I read application Help topics?

Security updates for Windows operating systems have introduced new security features that interfere with the operation of compiled HTML help files (*.chm) accessed across a network. "Action Canceled" or "Page cannot be displayed" error messages will appear in place of help topics in the Help viewer window.

Recent versions of Clone Manager can access HTML Help files on local computers, in place of help files in the network program installation directory. Ask your network administrator to make the compiled help file CM10Help.chm (CMSuite9.chm or Clone9.chm for version 9 software) available for you to copy to your home directory. (In Clone Manager, click File, Preferences, Basic to identify the location of your home directory, if needed.)

Once the help file is placed in your home directory, you can start Clone Manager and use the Help button within the Clone Manager program.

You can also download a new help file from this web site, if needed. In the Downloads section, click on Clone Manager User Documents and select the appropriate help file. You may need to unblock this file after download. Please follows the instructions on the download page.

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How can I export the sequence of a primer I've just designed?

With the primer open in the primer viewer window, click the Info tab and then click the toolbar button Export Primer Sequence. Select the option to export the primer sequence to a disk file or to copy the primer sequence to the Windows clipboard so that you can paste the primer sequence into another application. If your primer is a part of a primer collection, just open the Primer List and select (highlight) this primer in your collection. Click the toolbar button Export Primer Sequence and select to export to a disk file or copy to the clipboard.

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What's the quickest way to create a PCR amplified product?

In Clone Manager Professional, click Primer, Create Product to create a new DNA molecule that is the amplified product of a PCR-type reaction using two primers and a DNA molecule that you specify. Select the molecule and then select the two primers and click OK. If an amplified product can be produced, the results screen will show the product size, GC content, melting temperature and annealing temperature. You can select to use the new molecule now, save it to disk for later user or export the product sequence as a text file.

If an amplified product can not be produced using standard PCR reaction conditions, you can opt to relax these conditions and try again. If more than one product is possible, you can opt to open the Analyze Mix Wizard to view the more detailed results and then use the Create Product toolbar button in the results section to create the product of interest.

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How can I import a primer collection?

In Clone Manager Professional, you can use the Import option to create a primer collection by reading in primer data contained in a tab-delimited text file prepared in another application. Open the Primer List and click My Collections. Click the first toolbar button (Folder Options) and select Import. In the import module, select the text format file that contains your primer data. Follow the screen prompts to identify the data in each column and the first row to start importing.

Preparing data for import -- If your primer data is in an Excel worksheet, for example, you can open the worksheet in Excel and use Save As... to save your file in Text (tab delimited) format.

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