FAQ

Frequently Asked Questions

 

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Lasergene Core Suite


General 

» How do I use sequence files from other software packages in Lasergene? 
Many of the Lasergene applications will import sequences in multiple file formats. Click here for a list of import types by application. If a file type is not listed in your application of choice, you should open it in SeqBuilder and either save it in the Lasergene sequence file format (*.seq) or select File>Send Sequence To to open it in the application of your choice.

In addition, when you perform BLAST or Entrez searches using Lasergene applications, you can enter your choice of sequences from the match list directly to the Lasergene application. When you choose this option, Lasergene applications also save a copy of each sequence as a file in Lasergene format. You may also use the sequence's accession or ID number to directly download the data from NCBI and automatically open it into the Lasergene application.
» How do I use the synchronous updating feature within Lasergene? 
To utilize synchronous updating, simply open the same file in more than one application. Any edits that would affect the presentation of that sequence in the other application will appear when you bring the other application to the front (i.e. in focus).
» How do I search BLAST or Entrez text databases within Lasergene? 
To utilize BLAST, simply highlight a sequence region and select Blast Selection from the Net Search menu. Then from the BLAST query window, select the server URL (if not the default), the BLAST program, and database to search. A window will appear displaying the BLAST search results.

To utilize the Entrez text query builder, simply select New Text Search from the Net Search menu. Select the Entrez text server you want to query, pick the database, then construct your query. A window will appear displaying the Entrez search results.

» Why does the error "A different version of Lasergene is running" appear, but I don't have another version running? 
If you receive the error "A different version of Lasergene is running" when you try to launch a Lasergene application, but another version of Lasergene actually isn't running, there may be a lingering *.state file from another version that needs to be deleted.

The solution is to locate and delete the following files:

STARDM.state
STARDM2.state
STARDM7.state
STARDM8.state
STARDM9.state
STARDM10.state

These files may exist in the following directories:

Macintosh:
Hard Drive:Library:Preferences:DNASTAR:DataManager
Hard Drive:Users:username:Library:Preferences:DNASTAR:DataManager

Windows Vista, Windows 7 and Windows 8:
C:\Users\username\AppData\Local\DNASTAR\DataManager
C:\ProgramData\DNASTAR\DataManager

Windows XP:
C:\Documents and Settings\username\Application Data\DNASTAR
C:\Documents and Settings\All Users\Application Data\DNASTAR\DataManager

If you find any of the *.state files listed above, delete them. Once the files are deleted, the error should no longer appear.
» How do I change the default application for opening my Lasergene files? 
On Windows XP:
1. Open the Control Panel and go to Folder Options.
2. Select the File Types tab.
3. Select extension you wish to change in the Extensions list and then click the Change button.
4. Click the Browse button in the Open With dialog box.
5. Navigate to and select the application you want the files to open in. (Lasergene applications are located by default in C:\Program Files\DNASTAR\Lasergene 10).
6. Click Open.
7. Click OK to close the Open With dialog box.
8. Click Apply and then Close.

On Windows Vista, Windows 7 and Windows 8:
1. Open the Control Panel.
2. Go to Programs>Default Programs>Associate a file type or protocol with a specific program.
3. Select extension you wish to change in the Extensions list and then click the Change program button.
4. Click the Browse button in the Open With dialog box.
5. Navigate to and select the application you want the files to open in. (Lasergene applications are located by default in C:\Program Files\DNASTAR\Lasergene 10 or C:\Program Files (x86)\DNASTAR\Lasergene 10).
6. Click Open.
7. Click OK to close the Open With dialog box, and then click Close.

On Macintosh:
1. Select a file of the type you wish to change in Finder.
2. Go to File>Get Info.
3. Click the dropdown arrow in the Open With field, and navigate to the application you want the files to open in. (Lasergene applications are located by default in Applications:DNASTAR:Lasergene 10).
4. Click the Change All button to make the application you selected the default for all files of this type.
» Why does it take so long for my Lasergene application to open on Macintosh OS X 10.7? 
Macintosh OS X 10.7 has a new built-in feature called “Resume.” If you close an application without closing its open document first, then re-open the application, Macintosh directs the application to resume where it left off. This new behavior affects all Lasergene applications except Protean 3D. If you were working on a large project when you closed an application (e.g. a SeqMan or SeqMan NGen assembly), it may take several minutes for the document to re-open.

Here is a work-around that may help in some cases:
  • Go to System Preferences > General and uncheck the option Restore Windows when quitting and re-opening apps.
  • In the same dialog, lower the Number of recent items for Applications, Documents and Servers to “None.”
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    » How can I change the default printing size? 
    Unless otherwise specified on your computer, the default printing size for all DNASTAR applications is “U.S. Letter” size (8.5 x 11 inches = 21.6 x 28 cm). You can temporarily change to another size, such as A4, from within the application. However, the next time you print, the default size will again be U.S. Letter size.

    To correct this issue, you need to change your computer’s default printing size:

    On Windows Vista, Windows 7 and Windows 8:
    1. 1. Open the Control Panel.
    2. 2. In the Hardware and Sound category, click on Printers or View devices and printers.
    3. 3. Right-click on your printer and choose Properties.
    4. 4. In the General tab, click on the Printing Properties button.
    5. 5. In the ensuing Printing Shortcuts tab, choose the desired default printing size from the Printing Sizes drop-down menu.
    6. 6. Click the Apply button, then the OK button.
    On Macintosh:
    1. 1. Open System Preferences.
    2. 2. Click on Print & Fax.
    3. 3. Choose the desired size from the Default paper size drop-down menu.

    Note: Changes to the default printing size will not be applied until after you restart the DNASTAR application.

    SeqBuilder 

    » How do I create a custom Gateway vector to use in SeqBuilder? 
    Use the following steps to create a custom Gateway vector to use in SeqBuilder:

    1. Open your vector sequence file and make sure it is set to circular by selecting SEQUENCE>Circular.

    2. Add misc_recomb features to your sequence on the appropriate sub-sequences where recombination occurs. Note that while it is preferred for the entire recombination site to exist within your sequence, SeqBuilder at minimum requires the appropriate att core sequence for each of the five types of recombination sites. SeqBuilder uses these core sequences along with the feature labels to correctly identify each Gateway plasmid:

    • Type 1: GTACAAA (top strand)
    • Type 2: CTTGTAC (bottom strand)
    • Type 3: ATTATAC (bottom strand)
    • Type 4: GTATAGA (top strand)
    • Type 5: GTATACA (top strand)

    3. Label the features as follows:

    • For Expression Clones: attB1, attB2, attB3, attB4, and attB5
    • For Donor Vectors: attP1, attP2, attP3, attP4, and attP5
    • For Entry Clones: attL1, attL2, attL3, attL4, and attL5
    • For Destination Vectors: attR1, attR2, attR3, attR4, and attR5

    Note: The classic Gateway cloning protocol uses only types 1 and 2 of recombination sites. MultiSite Gateway technology utilizes all 5 types of recombination sites, which allows you to recombine multiple regions at one time.

    4. Save your sequence file.

    Once this is done, you can add your custom vector to the catalog so that it can be used in all projects:

    1. Select FILE>Open.

    2. Select the vectors catalog, CloningVectors.sbp,found in the following directory:

    Windows XP: C:\Documents and Settings\All Users\Shared Documents\DNASTAR\Lasergene 10 Data
    Windows Vista, Windows 7 and Windows 8: C:\Users\Public\Public Documents\DNASTAR\Lasergene 10 Data
    Macintosh OSX: Hard Drive:Applications:DNASTAR:Lasergene 10 Data

    3. Expand the Gateway Vectors folder, then select the appropriate sub-folder, depending on the type of custom vector you are adding.

    4. FILE > Import Sequence(s) to Project and navigate to your custom vector sequence file. Selecting this sequence file will add it to the vector folder you selected.
    » How do I use the Cloning Vector Catalog? 
    Lasergene has a set of vectors that you can use for cloning. They are contained in a cloning project called CloningVectors.sbp. This file can be found in the following directory:

    Windows XP: C:\Documents and Settings\All Users\Shared Documents\DNASTAR\Lasergene 10 Data

    Windows Vista, Windows 7 and Windows 8: C:\Users\Public\Public Documents\DNASTAR\Lasergene 10 Data

    Macintosh: Hard Drive:Applications:DNASTAR:Lasergene 10 Data

    You may use any of the vectors from the catalog in your cloning projects. Simply create a new cloning project FILE>New Cloning Project, and then drag and drop (or copy and paste) the desired vectors from the catalog into the desired folder in your new cloning project.

    For directions on how to add vectors to the cloning vector catalog, click here.

    DNASTAR updates the cloning vectors catalog with each new release. Note that if you customize your cloning vectors catalog, then Lasergene will not overwrite your customized file with the new catalog when you install a new version of Lasergene.

    » How can I export my linear or circular map to another application such as Microsoft Word, or Adobe Illustrator? 
    With the graphical view you want as the active window, choose Edit>Select All, then Edit> Copy as Picture. The graphical view is then copied to your clipboard and can be pasted into another application.

    Note: in Microsoft Word and PowerPoint, be sure to select Edit>Paste Special then select Picture (Enhanced Metafile).

    Once the view is pasted in an application as a picture, you can resize by dragging the sizing handles.
    » How do I get my linear map in one continuous line on my page? 
    To view your linear map in one continuous line, go to File>Page Layout and change the Groups per Page to 1.
    » How do I change the font of my sequence? 
    Double-click on either the top or bottom strand of your sequence to highlight it. Then go to Format>Font to change the font of your sequence or to Format>Size to change the size.
    » How do I create enzyme filters? 
    To create a new enzyme filter:

    1. Go to Enzymes>New Selector. This will open the Enzyme Selector Manager dialog box.
    2. Enter a name for the new selector and choose the type of selector this will be (Class, Overhang, Frequency, Pick, or Combine).
    3. Choose the criteria that will be used when this selector is employed by using the options on the Enzyme Selector Manager.
    4. Click Evaluate to add the criteria to the new selector. In most cases, enzymes that will be selected by the selector appear in the Result box on the right side of the Enzyme Selector Manager dialog.
    5. Click OK to create the selector. The new selector may now be chosen in the Enzymes Displayed>Filter by Selectors subfolder in the curtain.
    » How do I add a vector into the Cloning Vector Catalog? 
    From within SeqBuilder, go to File>Open and select CloningVectors.sbp, which is the vectors catalog. This file can be found in the following directory:

    Windows XP: C:\Documents and Settings\All Users\Shared Documents\DNASTAR\Lasergene 10 Data

    Windows Vista, Windows 7 and Windows 8: C:\Users\Public\Public Documents\DNASTAR\Lasergene 10 Data

    Macintosh: Hard Drive:Applications:DNASTAR:Lasergene 10 Data

    Then, do one of the following:

    i. If the vector file is a sequence file, click on one of the folders, select File>Import to navigate to the file you want, and then double-click the sequence to open. A copy of the sequence(s) in that file are added to the catalog.

    ii. Alternatively, if the vector file is a sequence file, open the file, select File>Add Sequence to Project. A copy of the sequence file is added to the catalog.

    iii. If the vector file is in another project file, open that project by selecting File>Open and selecting your project. Copy and paste the file from the project to the Cloning Vector Catalog.

    Then, go back to the CloningVectors.sbp window and select File>Save.

    For directions on how to add custom Gateway vectors to the cloning vector catalog, click here.

    For directions on how to add custom vectors for Directional TOPO or TA Cloning to the cloning vector catalog, click here.
    » How do I import my Vector NTI database? 
    SeqBuilder offers a one-step batch import of Vector NTI DNA (*.gb) and protein (*.gp) files, as well as Vector NTI database archives,*.ma4 and *.pa4 files.

    To import your Vector NTI sequences, simply open a new SeqBuilder project (go to File>New Project). You can create and organize folders within the Project window to suit your preferences. Then, import *.gb and *.gp files either from their saved location or from the Vector NTI database by simply highlighting the sequences (using Shift+Click), then dragging and dropping them into the appropriate folder in the SeqBuilder Project window. Import *.ma4 or *.pa4 files by locating them in their saved location, then dragging and dropping them into your SeqBuilder project window. SeqBuilder sequence files will be created for each of the Vector NTI files dragged into the folder.

    After your sequences have been imported, you may see the imported features by opening an sequence and checking the Features Displayed box in the curtain that appears on the left side of your screen. Likewise, to view the enzymes for your sequence, first expand the Enzymes Displayed folder from the curtain. Then, you may either select them individually from the All Enzymes - Alphabetical list, select a group of enzymes by using one of SeqBuilder's enzyme selectors from the Filter by Selector list, or create your own enyzme filter by selecting ENZYMES>New Selector.

    Note for MacIntosh Users: Vector NTI only runs on operating systems up to OS 10.3. Lasergene 9 is supported only on OS 10.5 and higher. If you are using Vector NTI on OS 10.3 or earlier, you must first archive your sequences as a *.ma4 or *.pa4 file. Then, you can upgrade your OS to a current version, and import your *.ma4 and *.pa4 files as described above.
    » I renamed my SeqBuilder file, but when I open it the old name still appears. Why? 
    If you rename your SeqBuilder file outside of a Lasergene application, the sequence inside the file is not actually renamed. For example, if you right-click on the file from where it is saved on your computer, and choose "Rename," the original name of the sequence will still be displayed when you open the file again in SeqBuilder.

    To rename a SeqBuilder file, open the file in SeqBuilder and choose File>Save As.

    Note: This also applies to Protean and GeneQuest files.
    » How do I create a custom vector to use with Directional TOPO or TA Cloning? 
    Use the following steps to create a custom vector to use with Directional TOPO or TA Cloning:

    1. Select FILE > Open to display the sequence that you want to create as a new vector.

    2. Highlight the portion of the sequence that you want to use as a vector.

    3. Hold down the Alt (Windows) or Option (Mac) key and do one of the following:

    To create a T-Vector: Select the Create TA Cloning Insert to add the linearized T-vector to the front-most project.
    Or
    To create a Directional TOPO vector: Select the Create Directional TOPO Insert to add the linearized TOPO vector to the project.
    » How do I change my default page size for printing? 
    To change the default printing settings in SeqBuilder, such as paper size, you must change your computer’s printing preferences.

    On Windows XP, open the Control Panel and select Printers and Faxes. On Windows Vista, Windows 7 and Windows 8, open the Control Panel and select View devices and printers. Next (all Windows systems), right-click on your printer and select Properties. In the resulting Properties window, click the Printing Preferences button to adjust your preferences. For default paper size, select the Paper/Quality tab.

    On Macintosh: Open System Preferences and choose Print & Fax. Adjust the paper size in the field “Default Paper Size in Page Setup.”

    SeqMan 

    » How can I view my chromatograms in my SeqMan project? 
    Go to Project>Alignment View, then click on the triangle next to each sequence to view your trace data. Alternately, use Alt/Option + click (Win/Mac) on any sequence triangle to open or close all the chromatograms at once.
    » What are the Q scores? 
    Q Scores are the quality scores that SeqMan assigns to each peak in your trace data. The quality score (Q) of a peak is calculated based on the shape and height of each peak, and is adjusted relative to the maximum height of any peak in the entire sequence. Taller, sharper peaks receive the highest quality scores. The heights of any underlying peaks are subtracted from the highest peaks score.
    » How do I adjust my trimming parameters? 
    Trimming parameters can be adjusted from the Unassembled Sequences windows by clicking the Trim Ends button or, by going to Project>Parameters and selecting End Trimming from the left side of the screen. End trimming can be based on Quality scores or by Fixed endpoints.
    » How do I save my Primer Walking Report? 
    With your Primer Walking Report open, go to File>Save Primer Info. You may save your primers as either a tab-delimited file (*.txt) or as a FASTA file (*.fas).
    » How do I change my primer parameters for Primer Walking? 
    Go to Project>Parameters and select Primer Walking from the list on the left. Here you can change the parameters for Primer Length, Salt Concentration, and Temperature for delta-G Calculations, as well as other characteristics.
    » How do I view all of my found primers and the contig? 
    Go to Contig>Strategy View. Your primers will be shown as green and red lines above and below your contig.
    » Why are my SNPs different colors? 
    The default colors are gray for Not a SNP, blue for Putative SNPs, green for Confirmed SNPs, and red for Rejected SNPs. Note that all reference SNPs are colored as Confirmed SNPs. To change any of these colors, go to Project>Parameters, select SNP Discovery and then click on any of the color boxes and choose from the color palette. Click OK when you are done; click Restore to return to the default colors.
    » How do I choose which assembly method to use? 
    SeqMan provides two different assembly methods: the Classic assembler, and the Pro assembler.

    In general, the Pro assembler should be used when your data is: 1) large; 2) contains repeated sequences; 3) has noisy ends; or 4) being used for SNP analysis.
    The Classic assembler should be used when: 1) your data does not contain repeated sequences; 2) you do not use vector trimming; or 3) you want to reproduce an assembly made from a previous version of SeqMan.

    As with all SeqMan parameters, you may select one of these assemblers as your default assembly method. You may also switch between the Pro and Classic assemblers with each SeqMan project.

    Note that if you are assembling next-gen data or very large data sets, you may also want to consider using SeqMan NGen.
    » How can I see my features in SeqMan? 
    Features on the constituent sequences in your assembly can be viewed from the Alignment View by clicking the triangle to the left of the sequence name. Features that have been added to the consensus sequence are viewed in the Strategy View beneath the Depth of Coverage Graph. All of the features in your project can be viewed and managed from the Feature Table (Features>Show Feature Table).

    If you are unable to see features within your project, it may be due to one of the following reasons:
    • »You may be looking for features on the consensus sequence from the Alignment View. Features that have been added to the consensus sequence will only be displayed in the Strategy View. To open the Strategy View, select Contig>Strategy View.
    • »The feature may have been on part of the sequence that was trimmed as vector.
    • »You may be viewing the Feature Table for the consensus sequence rather than for the constituent sequences, or vice versa. To display the Feature Table for the consensus sequence, first open the Strategy View by selecting Contig>Strategy View, and then select Features>Show Consensus Feature Table. If the Strategy View is not the active window, selecting Features>Show Feature Table will display features for the constituent sequences in your project.
    • »If the Scaffold Strategy View is open while you create a feature from the Strategy View (Features>New Consensus Feature), the Scaffold Strategy View will need to be closed and reopened before the new feature is displayed.
    » How do I get all my sequences into one contig? 
    To force all of your sequences into one contig, you may need to relax the Assembly parameters. To do this, go to Project>Parameters, and select Assembling from the left side of the screen. After selecting an assembly method, you can adjust the Match Size, Minimum Match Percentage, and Minimum Sequence Length, as well as several advanced parameters.
    » Why isn’t the coverage depth consistent between the Coverage Report and the Alignment View? 
    In the Coverage Report, the “Depth” column may not match the depth of coverage seen in the lower portion of the Alignment View. For instance, the Coverage Report may show a depth of “3” for a particular range even though you can see 5 or more sequences in the same range of the Alignment View. The apparent discrepancy occurs because the Coverage Report shows the minimum depth of coverage for a location, while the Alignment View shows all sequences that contribute to the coverage.
    » My SeqMan NGen assembly used multiplexed data. Why is the “MID” column missing from the SeqMan Pro SNP Report? 
    In order for SeqMan Pro to display the MID column in the SNP Report, you must choose either the diploid bayesian or haploid bayesian method of SNP calculation prior to assembly in SeqMan NGen. This can be done from the following dialogs:
  • Assembly Options dialog > Advanced Assembly Options button > SNP tab > SNP calculation method drop-down menu = Diploid bayesian or Haploid bayesian.
  • Recalculate SNPs > SNP Options button > SNP calculation method drop-down menu = Diploid bayesian or Haploid bayesian.
    • If you instead choose the “simple percentage” method for SNP calculation from the drop-down menu, the MID column will be omitted from the SNP Report.

    MegAlign 

    » How can I edit my alignment? 
    After completing a multiple alignment, you may manually realign portions of the alignment using the Straighten Columns, Shuffle Right and Shuffle Left palette tools. Straightening aligns selected residues from different sequences by insertion of gaps to the left of the selected residues. Shuffling is when residues are moved from one end of a gap to the other.
    » How can I export my phylogenetic tree? 
    With the phylogenetic tree as the active window, choose Edit > Copy. The tree is then copied to your clipboard and can be pasted into another application.

    Note: in Microsoft Word and PowerPoint, be sure to select Edit>Paste Special then select Picture (Enhanced Metafile).

    Once the phylogenetic tree is pasted in an application as a picture, you can resize by dragging the sizing handles. If you want to make changes to the image, select the Ungroup option from within your alternative application to be able to edit individual legends, labels, boxes, etc., or resize/delete them.
    » How can I export my Alignment Report? 
    The Alignment Report in MegAlign can be copied and pasted into another application as an image. To do this:

    1. Select View>Alignment Report.

    2. Select Edit>Copy.

    3. Paste the report to another application:

    For applications that offer both Paste and Paste Special options, we recommend you use Paste Special. In Microsoft Word or PowerPoint, for example, you will then be offered several options for pasting the clipboard contents (e.g., Metafile, Enhanced Metafile, or Unformatted Text). Enhanced Metafile is often the best option to use when pasting the Alignment Report and its decorations and histograms as a graphic object, although we suggest you experiment with the various choices.

    Choose Unformatted Text if you just want the aligned text for the sequences and the consensus.

    4. Once the report is pasted in an application as a picture, you can resize by dragging the sizing handles.

    Note: If you only want the text of the Alignment Report and not the decorations, you may prefer to save the alignment report as a text file by selecting File>Save As.
    » Why do I receive an "Insufficient Memory" error when aligning my sequences using the Jotun Hein method? 
    The Jotun Hein method is designed for aligning modest numbers of closely related proteins of short to moderate length. It is not intended for DNA alignments. Occasionally, if you try to align DNA with this method, you will receive a "insufficient memory" error. The solution to this is to use a different alignment method such as Clustal V or Clustal W.

    GeneQuest 

    » How can I map multiple sequences to a template in GeneQuest? 
    The DNA Finder method in GeneQuest allows you to find DNA regions within your sequence that match those in the sequence files you specify. GeneQuest uses the selected files to search both the top and bottom strands of your sequence.

    To apply the method:

    1. Double click on the method name (Gene Finding - DNA Finder) in the Method Curtain to open the Add Sequences dialog.

    2. Locate and select the appropriate sequence files. Note that you may select multiple sequences, and of a variety of file types, including Lasergene *.seq files, Lasergene project files from MegAlign, PrimerSelect, SeqBuilder, and GeneQuest, FASTA files, ABI or SCF trace files, SFF flowgram files, Phred files (*.phd), Zip files, DNA Multi-Seq Files (*.mseq), and File of Filenames (*.fof).

    3. Once you have selected the sequence(s) you wish to add, click Done.

    The top and bottom strand for each sequence you selected will now appear in the Method Curtain below the Gene Finding method. If you selected multiple sequences, a Composite top and bottom strand will also be listed. The Composite strands are created by superimposing all of the top/bottom strands for your specified sequences.

    4. Apply the desired strands to your assay surface by dragging and dropping.

    A hit is recorded when the match reaches or exceeds the minimum match size parameter (accessed by double-clicking on the Gene Finding method form the Method Curtain). Gap characters are not inserted in the identical region to extend an alignment. With this method, you can locate multiple matches for a sequence, as long as the areas are at least as long as the minimum match size.

    The score printed on the region plot indicates how many bases in the two sequences matched up. Using the Zoom In palette tool, zoom in until you see the numbers. Clicking once on the plot and holding the mouse button reveals the matching coordinates of the two sequence stretches, and tells whether the match occurred on the top or bottom strand. If you wish to see the residues for the match, continue using the Zoom In tool until the sequence is displayed.
    » Why does the method I just selected not display on my sequence? 
    To be applied to your sequence, methods need to be dragged and dropped onto the assay surface.
    » How do I enter a custom search pattern? 
    To search for a custom pattern, click on the More Methods menu, then Patterns> Type-in Pattern. Enter a name for your pattern, then type in the Pattern itself in the appropriate field. To incorporate inclusive expressions in your pattern, use square brackets around whichever bases are acceptable (e.g., "[CG]" means C or G is acceptable).

    For exclusive expressions, use curly brackets around whichever bases are unacceptable (e.g., "{AT}" means neither A nor T is acceptable). To avoid typing repeated expressions, type the base, followed by the number of repeats in parentheses (e.g., the pattern "AG(3)T" would search for the string AGGGT). For gapped expressions, type in the symbol X followed by the acceptable maximum number of gaps (e.g., the pattern "AX(1,3)G would recognize the following sequence strings: AXG, AXXG, AXXXG).

    Finally, set the Threshold to specify how many mismatches you will permit. This method will not gap a pattern unless it is part of the syntax. If you have used ambiguous characters or inclusive expressions, keep the Threshold high to avoid false matches.

    Protean 

    » Why does the method I just selected not display on my sequence? 
    To be applied to your sequence, methods need to be dragged and dropped onto the assay surface.

    PrimerSelect 

    » How can I use PrimerSelect to find the Tm and %GC of primers I already have? 
    From the PrimerSelect Log menu, choose Primer Catalog. Then enter primer information on a separate line for each primer in the Catalog. You can use copy and paste if you already have the primer sequence in electronic form. The Tm and %GC will be calculated for each primer as it appears in the catalog.

    Primer Catalogs may also be created within SeqBuilder, or completely outside of Lasergene. The Primer Catalog is a tab-delimited text file with the extension of .pri that can be created using Microsoft Excel where the first column contains the sequence, the second the primer name and the third (optional) notes about the primer.

    When you want to know if your current collection of primers may be suitable for a particular template sequence, either add the primers directly to the Primer Catalog or use File>Open to use the externally created Primer Catalog. Then, enter the template sequence into PrimerSelect, and choose Locate>Only Catalogued Primers.
    » How are primer pair scores calculated? 
    Primer pair scores are calculated based on four factors: Product Length, Primer Tm Match, Product Tm Difference, and Stability Profile, and weights each score based on the importance assigned to each factor. Scoring also takes into consideration your Ideal Product Length. To view the default values for scoring parameters, go to Locate>Adjust Scoring. Your Ideal Product Length and the importance of each factor can be adjusted here by moving the sliding rulers. Alternatively, you may also adjust these values under the Set Values button.
    » How do I search a specific region of a sequence for primers? 
    You can specify certain regions of a sequence for PrimerSelect to look for primers. To set these, go to Conditions>Primer Locations. Choose to restrict primer locations by "Upper and Lower Primer Ranges" then type in your range for the upper and lower primers.
    » How do I export primer sequences? 
    You can export primer sequences from PrimerSelect by entering them into a Primer Catalog, and then saving it as an auxiliary primer catalog. With your Primer Catalog open, choose File>Save As. Select "primer catalog" when asked what it is you want to save. This will save your catalog as a Primer Catalog file type (*.pri) which is in a tab-delimited format. This file can then be opened in SeqBuilder, or in an external program that reads tab-delimited files, such as Microsoft Excel.
    » Why doesn't PrimerSelect report a dimer identified by another program? 
    Dimerization negatively affects pairing with the template when it occurs at the 3' end of the primer where the polymerase binds, but has much less of an impact when it happens further away. For this reason, PrimerSelect enables you to control the distance from the 3' end of the primer where dimerization is considered. Ignoring duplexing at a set distance from the 3' end allows PrimerSelect to identify many otherwise useful primers.

    To access this parameter, select Conditions>Primer Characteristics. By default, PrimerSelect ignores hairpins and dimers that occur 8 bp from the 3' end.

    GenVision 

    » I'm trying to use the GenVision Plug-In, but I don't see "GenVision Dialogs" under the Windows menu in Adobe Illustrator. Why? 
    During GenVision installation, you may have been prompted to locate the "Plug-ins" folder for Adobe Illustrator. If you did not receive a prompt, or if you did not choose the correct directory, you will need to move the plug-in file manually. Copy GenVision. aip from C:\Program Files\DNASTAR\Lasergene 10 or C:\Program Files (x86)\DNASTAR\Lasergene 10 (Windows) or Hard Drive:Applications:DNASTAR:Lasergene 10 (Macintosh) and paste it into the "Plug-ins" folder for Adobe Illustrator.

    Once the file is in the correct folder, you should have access to the Windows>GenVision Dialogs menu option within Illustrator. If you have placed the file in the correct directory and still do not see this menu option in Illustrator, it is possible that Illustrator was open during the GenVision installation. If this is the case, simply close and then relaunch Illustrator.
    » I added a scale to my image, but the numbers are so big that they overlap each other. How can I fix this? 
    Each panel's size in a GenVision image is relative to all of the panels in the image. As panels are added to the image, each panel will get smaller. As panels are removed from the image, each panel will get larger.

    If the scale (or any panel) appears too large, first continue adding all of the desired panels to your image. Once all of the panels have been added, if a panel is still larger than you prefer, then you will need to decrease the Relative Size value for that panel.

    To adjust the Relative Size value for a panel using the GenVision standalone application:

    1. From the Map Data pane, first select the panel you wish to change by clicking on its row.
    2. Click the Edit button to open the Edit dialog for that panel.
    3. Decrease the Relative Size value, and then click OK.

    To adjust the Relative Size value for a panel using the GenVision Plug-In:

    1. Access the Panels dialog by selecting Windows>GenVision Dialogs>Panels.
    2. Select the panel you wish to change by clicking on its row.
    3. Decrease the Relative Size value at the bottom of the Panels dialog, and then press Enter.
    » Why can't I see the panel I just added to my image? 
    Check to make sure that the color of the items in the panel (text, graph lines, etc.) are not the same color as your background color.
    For most panels, color can be specified either in the panel data file, or in the panel dialog. Note that colors specified in the data file always take precedence over colors specified in the panel dialog.

    To change the background color for your image using the GenVision standalone application, click on the Page Layout tab and then click the Background button to edit the color.

    To change the background color for your image using the GenVision Plug-In, access the Defaults dialog by selecting Window>GenVision Dialogs>Figure Defaults. Then, click the Background Color button to edit the color.
    Check to make sure that the data in your panel is not outside of the Display Range you have specified.
    The Display Range Start and End coordinates indicate the range of data you wish to display in your image. If the data coordinates in a particular panel are outside of this range, the panel will not be displayed on your image. You can check the data coordinates for a panel by reviewing its corresponding data file.

    In the GenVision standalone application, the Display Range fields are found in the Map Data pane.

    In the GenVision Plug-In, the Display Range fields are found in the Figure Settings dialog.
    » When I view my linear map in a Post Script viewer, why is my text panel cut off on the left margin? 
    The text panel in your image may be too big. To fix this problem, decrease the Relative Size of the panel. Additionally, it may also help to change the orientation of your text.

    To adjust the Relative Size value for a panel using the GenVision standalone application:

    1. From the Map Data pane, first select the panel you wish to change by clicking on its row.
    2. Click the Edit button to open the Edit dialog for that panel.
    3. Decrease the Relative Size value, and then click OK.

    To adjust the Relative Size value for a panel using the GenVision Plug-In:

    1. Access the Panels dialog by selecting Windows>GenVision Dialogs>Panels.
    2. Select the panel you wish to change by clicking on its row.
    3. Decrease the Relative Size value at the bottom of the Panels dialog, and then press Enter.

    To adjust the orientation of your text using the GenVision standalone application:

    1. From the Map Data pane, first select the panel you wish to change by clicking on its row.
    2. Click the Edit button to open the Edit dialog for that panel.
    3. From the Alignment drop-down list, select a new orientation (vertical, right, center, etc.) and then click OK.

    To adjust the orientation of your text using the GenVision Plug-In:

    1. First make sure the Text dialog is open by selecting Window>GenVision Dialogs>Text.
    2. Then, access the Panels dialog by selecting Windows>GenVision Dialogs>Panels.
    3. Select the panel you wish to change by clicking on its row.
    4. From the Text dialog, click on the Orientation button you desire (vertical, right, center, etc.), and then press Enter.
    » When viewing a GenVision project in Adobe Illustrator, a small red box with a plus symbol appears in the legend. Why? How can I remove it? 

    This issue may occur after you create a map in SeqBuilder and use FILE>Export as GenVision Project. When you open the resulting .gnv file in Illustrator, a small red box with a plus symbol may replace some of the letters in the legend, particularly the letters “r” or capital “i.” This red box character affects legend components such as enzyme and sequence names.


    Illustrator may experience problems drawing text in proportionally-spaced fonts when the text goes outside the clipping region. The red box character is a symptom of the path length being too small to contain all the text. Consult the Adobe webpage on overflow text for more information.


    This issue may occur if you are using GenVision Plug-in version 2.0 or earlier.


    This issue should not occur:

    • If you are using GenVision Plug-in version 2.0.1 or later in combination with Illustrator CS3, CS4 or CS5.

    • If you are using the GenVision Utility or GenVision Standalone to view the .gnv file.


    How can I fix this issue?

    The most effective way to fix the issue is to login and download the most recent version of GenVision. Alternatively, open the .gnv file in Illustrator and:


    • Extend the clipping path of the legend by selecting the Illustrator Selection Tool (V) and clicking on one of the red box characters. Click and drag the sides and/or corners of the resulting blue rectangle to increase the path size.


    • Change the font or font size of the legend text by selecting the Illustrator Type Tool (T) and clicking on the text where the red box character appears. Then do one or both of the following:

    - Right-click, choose Size, then select a smaller font size from the list.

    - Right-click, choose Font, then select a fixed-width font (e.g. Courier New) from the list.
    » Why am I receiving the error message "Windows cannot find AcroRd32.exe"? 

    This issue occurs on Windows operating systems if you uninstall your default PDF viewer.




    To resolve this issue, follow the numbered steps from the GenVision FAQ entitled:  I'm using the GenVision plug-in for Adobe Illustrator.  Why am I receiving the error messages "No application is associated with the specified file" and "This file does not have a program associated with it"?
    » I'm using the GenVision plug-in for Adobe Illustrator. Why am I receiving the error messages "No application is associated with the specified file" and "This file does not have a program associated with it"? 
    This issue has been observed when using the GenVision 2.0 plug-in on the Windows operating system. One or both of the following messages are displayed after making a change or adding a panel.





    The issue can be caused by invalid or missing file associations for PDF files. It can also occur if you are using Adobe Reader X with Use default viewer for .pdf files selected in the GenVision Options dialog.

    To resolve this issue, follow these steps:

    1. 1. Verify that Adobe Reader has been installed.
    2. 2. Open GenVision.
    3. 3. Select VIEW > Options.
    4. 4. In the dialog, check View output as PDF.  Directly under that checkbox, choose Use this program to view output.
    5. 5. Click the associated Browse button, and navigate to the Adobe Reader application or to the Adobe Reader desktop shortcut.  Click Open.
    6. 6. Uncheck View output as PostScript.
    7. 7. Click OK.

    If you continue receiving the same error messages after performing these steps, we recommend installing a different PDF program, such as Sumatra PDF.

    SeqNinja 

    » When performing multiple calculations in a single program, why do I get unexpected results? 
    When running a SeqNinja program where the input file for one step is the output file from an earlier step, you may obtain unexpected results. Specifically, the final output may have additional sequences and/or features.

    Here is an example of a workflow that can lead to such unexpected results:

    PROGRAM A
  • Step 1: Extract features from TEST.GBK and save them as EXTRACTED.GBK.
  • Step 2: Translate EXTRACTED.GBK and save the results as TRANSLATED.GBK.
  • Result: The file TRANSLATED.GBK may contain unexpected data (e.g., an extra translated feature).
    • This situation arises when there are overlapping CDS features. In such cases, a piece of one CDS will end up being annotated in the interval it shares with the second CDS. Then, when the EXTRACTED.GBK file is translated, that particular sequence will result in two protein sequences: the desired full length CDS, and the fragment of the overlapping CDS. Note that this is not an issue when the intermediate file is in FASTA format, since there is no carryover of information about the overlapping CDS.

    For cases in which the extracted features are desired in GenBank format, we recommend writing two separate programs rather than using the output from one step as the input for a later step.

    PROGRAM A
  • Extract features from TEST.GBK and save them as EXTRACTED.GBK.
    • PROGRAM B
  • Translate EXTRACTED.GBK and save the results as TRANSLATED.GBK.
  • Result: The file TRANSLATED.GBK contains the expected data.
    		•

    Protean 3D / NovaFold 

    » Why is the Protean 3D screen blank on my Mac's Parallels Desktop? 
    The Protean 3D application launches, but all panes remain blank after opening a file. This issue has been observed when using Parallels Desktop 5 in combination with Microsoft Windows 7, but may also occur in other versions.
    To resolve this issue, enable 3D acceleration for Parallels Desktop. See this Parallels web page for instructions.
    » Why do the side chains temporarily disappear in the Structure View when I rotate or move the molecule? 
    If the molecule has 20,000 or more atoms, the side chains will temporarily disappear in the Structure View when you rotate or move the molecule. This circumvents slow-downs that would occur if the completely-rendered molecule was refreshed throughout the rotation or move. The side chains will appear again as soon as you stop rotating or moving the molecule.
    » I edited a *.structure file using SeqBuilder, but can't see the changes in Protean 3D. Why not? 
    When working with structures, Protean 3D always uses the sequence from the original PDB file. When a PDB file is saved as a *.structure file, two copies of the original sequence are stored in that file. The first copy—which is used whenever the file is opened in Protean 3D—cannot be edited. The second copy can be edited with SeqBuilder, and the edits can be viewed in any of the other Lasergene Core Suite applications.
    » Why do I get an error message when I try to download files from the Motion Library on Windows? 
    When attempting to download files from the Motion Library on Windows, you may receive the following error message: I/O error when communicating with DNASTAR Motion Library Server. This issue may occur if Windows Firewall is On and Outbound Connections are Blocked. Simply adding Protean 3D to the list of allowed programs is not likely to correct the issue. There are several possible work-arounds:
  • Download the entire Motion Library from our website.
  • Add one of these rules to the Windows Firewall Advanced Settings dialog, which is accessed through the Windows Control Panel’s “Security Settings”:
  • Allow Protean 3D to make outbound HTTP connections.
  • Allow Protean 3D to pass through the Firewall on port 80.
    • For more information on creating rules, consult Microsoft’s support page for Windows Firewall Advanced Settings.
    » How can I update the PROSITE database between releases of Lasergene? 
    You may update the PROSITE database at any time following the steps below:

    1) Go to this ExPASy web page, then select the Downloads tab from the top of the page.

    2) From the ftp directory, right-click on the file prosite.dat and select Save Link As.

    3) In the Save dialog, navigate to the appropriate folder for your operating system:
  • Windows Vista/Windows 7/Windows 8: C:\Users\Public\Documents\DNASTAR\Lasergene 10 Data\Prosite
  • Windows XP: C:\Documents and Settings\All Users\Shared Documents\DNASTAR\ Lasergene 10 Data\Prosite
  • Macintosh OS X: Applications:DNASTAR:Lasergene 10 Data:Prosite
    • 4) Click Save. When prompted, confirm that you wish to overwrite the existing prosite.dat file.

    The updated PROSITE database is now ready to use in Protean and Protean 3D. Before using the PROSITE database, please read the note near the top of the prosite.dat file regarding licensing for commercial entities.
    » I created a multiple-file Protean 3D project using Lasergene version 10.1 (or higher). Can my project be viewed and saved by another user who has Lasergene version 10.0? 
    If one user creates a Protean 3D project using Lasergene version 10.1 (or higher), then sends the results to a second user who has Lasergene version 10.0, the second user will be able to open the multiple-file project, and the information for all the structures will appear in the Explorer panel. However, only the first structure will be displayed in the Structure view, and the Analysis view will be disabled. If the second user saves the project in Lasergene version 10.0, all information regarding everything other than the first structure will be discarded.

    The only way the second user can access the full functionality of a multiple-file document is to upgrade to Lasergene version 10.1 (or higher).
    » How do I input my Amazon Web Services (AWS) credentials on the DNASTAR website? 
    You may opt to use your own Amazon Web Services (AWS) credentials to access NovaFold. To do this, you must login and then enter your credentials on DNASTAR's AWS page .

    For help creating or locating your AWS credentials, please refer to the Amazon Web Services website.