Lasergene Quick Tips – Molecular Biology

DNASTAR no longer supports Protean

Date: 10/11/17

 

Version Affected: 15.0 and later

 

Version Fixed: N/A

 

Issue: As of October 11, 2017, corresponding with the release of Lasergene 15.0, DNASTAR’s Protean application is being retired. We will continue to support Protean’s successor, Protean 3D, which contains the key functionality of the retired application.

 

Resolution: For assistance in upgrading to the latest version of Lasergene, including the Protean 3D application, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Attempt to check out commuter license on Mac leads to “Check Out Error” message

Date: 9/16/17

 

Version Affected: All

 

Version Fixed: N/A

 

Issue: For DNASTAR License Server configurations authorized after September 15, 2017, the commuter license manager on Macintosh may give the following message:

 

Check Out Error

Unable to check out

Error [125]: Required locking criteria for local request is not available on your machine.

.

Resolution: We are working to fix this issue. If you are experiencing an issue attempting to check out a commuter license on Macintosh, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

DNASTAR no longer supports SeqMan NGen on Linux

Date: 3/2/17

 

Version Affected: 14.1 and later

 

Version Fixed: N/A

 

Issue: As of March 2, 2017, corresponding with the release of Lasergene 14.1, DNASTAR no longer supports SeqMan NGen for the Linux operating system. We will continue to support SeqMan NGen for Windows and Macintosh.

 

Resolution: If you have questions about this change, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Issues with RNA-Seq or ChIP-Seq workflows on non-English Windows systems

Date: 6/12/17

 

Version Affected: 14.1 and earlier

 

Version Fixed: 14.1.2

 

Issue: Users running Windows machines with an active non-English language pack or with certain non-American region settings may experience issues (e.g. stalling or errors during assembly), particularly with RNA-Seq or ChIP-Seq workflows in SeqMan NGen.  These issues are partially related to the software not recognizing certain regional number settings: where characters other than a comma are used to separate groups of digits, or where characters other than a period are used for the decimal symbol.

 

Resolution: This issue has been addressed in the 14.1.2 patch released June 12, 2017. To avoid or correct this issue, please upgrade to the current version of Lasergene. For assistance, contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Note regarding Variant Annotation Databases based on GRCh37 and GRCh38

Date: 5/5/2017

 

Version Affected: 13.1 to 14.1

 

Version Fixed: NA

 

Issue: The Variant Annotation Database (VAD) based on human genome reference GRCh37 was first released with Lasergene 13.1 in March 2016. With the March 2017 release of  Lasergene 14.1,  a companion VAD version was added, based on human genome reference GRCh38. DNASTAR software automatically detects which version of the human genome reference sequence is used in a SeqMan NGen assembly and accesses the corresponding VAD for variant annotation.

 

The aforementioned Lasergene 14.1 release also included an update of the GRCh37 version of the VAD and the removal of Polyphen2 data from both VAD versions due to licensing issues.

 

In  May 2017, to address some data inconsistencies caused by changes in the reference sequence between the GRCh37 and GRCh38 VAD builds, the GRCh37 version was reverted to its pre-Lasergene 14.1 state. We also anticipate some cases in which annotations from the GRCh38 version of the VAD will be missing, due to the changes in the reference sequence.

 

Resolution: DNASTAR will continue to update the VAD periodically and will strive to address any remaining inconsistencies between the two versions.  In the interim, there may be cases where the data and annotations do not align as expected. For questions regarding this topic, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Protean 3D displays a NovaDock project as an empty document

Date: 6/1/2017

 

Version Affected: 14.1 and previous

 

Version Fixed: 15.0 (anticipated in Fall 2017)

 

Issue: Protean 3D may display an empty NovaDock report document (.novadock) when opening a prediction with user-defined proposed contacts with PDB insertion codes containing one or more alphabetical characters. Since Protean 3D incorrectly assumes that all residue identifiers will be integers, this leads to a visualization error. Note that the results created by NovaDock are still valid, even though they cannot be viewed in Protean 3D version 14.1 and previous.

 

Resolution: This issue will be resolved with the release of Lasergene 15.0, anticipated in Fall 2017. Until then, a workaround is to renumber any PDB files, prior to submission to NovaDock, such that user-defined contacts do not contain insertion codes. For questions, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

DNASTAR no longer supports Lasergene 11

Date: 3/2/17

 

Version Affected: Lasergene 11 (and earlier)

 

Version Fixed: N/A

 

Issue: As of March 2, 2017, corresponding with the release of Lasergene 14.1, DNASTAR no longer supports Lasergene 11 (or earlier).

 

Resolution: Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for assistance in upgrading to the latest version of Lasergene.

The Variant Annotation Database is not supported for new projects created in ArrayStar 14.0 or earlier

Date: 3/2/2017

 

Version Affected: 14.0 and earlier

 

Version Fixed: 14.1

 

Issue: With the release of Lasergene 14.1, ArrayStar’s online Variant Annotation Database has been updated to support human genome build 38, as well as build 37. In addition, Polyphen-2 scores and predictions are no longer supported. Due to these changes, Lasergene 14.0 and earlier will no longer allow downloading from the Variant Annotation Database when creating new projects. These changes do not affect existing project data or other ArrayStar functionality.

 

 

Resolution: In order for new ArrayStar projects to have access to the online Variant Annotation Database, you must update to Lasergene version 14.1 or higher. To do this, log in to your DNASTAR account and update to the most recent version of Lasergene . If you have questions or need assistance updating your software, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

Issues running Lasergene on Macintosh 10.12 (Sierra)

Date: 3/2/2017

 

Version Affected: 14.0 and earlier

 

Version Fixed: 14.1

 

Issue: Users of Lasergene 14.0 and earlier have experienced a variety of issues when running Lasergene applications on Macintosh 10.12 (Sierra). Several issues pertain to all Sierra machines, while others occur only on Sierra machines using the Retina high-definition display. Examples of known issues include:

 

  • Lasergene application help does not display.
  • Except in SeqBuilder, initiating a BLAST search causes the Lasergene application to close.
  • On Retina displays only, dialogs for adding, opening, saving or exporting files do not display correctly, or  cause the Lasergene application to close.

 

Resolution: These issues have been resolved with the release of Lasergene 14.1. To regain full software functionality, log in to your DNASTAR account and update to the latest version of Lasergene. If you have questions or need assistance updating your software, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

 

For best results, we also recommend updating your Macintosh machine to Sierra 10.12.4 when that version is released.

Issues related to NCBI’s transition from “http” to “https” URLs

Date: 9/29/2016

 

Version Affected: Version 13 and previous

 

Version Fixed: 14.0

 

Issue: By December 31, 2016, all U.S. federal government entities will be required to use secure “https” websites instead of general “http” websites. The National Center for Biotechnology Information (NCBI) has announced they plan to make this change on September 30, 2016. We anticipate that NCBI will disable some “http” functionality periodically through the end of 2016, and will disable most or all of it after the end of 2016.

 

NCBI’s changes will cause the following functions to be disabled in all versions of Lasergene through version 13:

 

  • BLAST searching and downloads (multiple applications)
  • Entrez searching and downloads (multiple applications)
  • Genome downloads from NCBI (ArrayStar)

 

The following Lasergene functions will work only as long as NCBI supports automatic redirects:

 

  • dbSNP links (SeqMan Pro and ArrayStar)
  • Protein Database (PDB) links (Protean 3D)

 

Resolution: This was fixed in Lasergene 14.0, which now directs communications to the new “https” URLs. To resolve the issue, log in to your DNASTAR account to update to the latest version of Lasergene. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

Issues related to NCBI’s transition from GI Numbers to Accession Numbers

Date: 9/29/2016

 

Version Affected: 13 and previous

 

Version Fixed: 14.0

 

Issue: The National Center for Biotechnology Information (NCBI) has announced that they are changing certain file formats and restructuring their EUtils databases. The date of this change has not been announced, but will likely occur in Fall 2016.

 

Many Lasergene applications allow you to search and download files from NCBI databases. The upcoming NCBI changes will affect BLAST/Entrez searching and Transcript Annotation Database functionality  in all existing versions of Lasergene (through version 13). For example, Lasergene currently utilizes NCBI’s present identification system of “Genome Identifier Number” (GI #) as the unique sequence identifier,  though “Accession Numbers” are also supported in many situations. As one of the changes, NCBI intends to begin using “Accession Numbers” as the unique sequence identifier.

 

Resolution: With the launch of Lasergene 14.0, all applicable Lasergene applications now support “Accession Numbers” as the unique sequence identifier. To resolve the issue, log in to your DNASTAR account to update to the latest version of Lasergene. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

Some samples may not be fully annotated with Variant Annotation Database information

Date: 7/11/2016

 

Version Affected: 13.0.0-13.0.2

 

Version Fixed: 13.0.3

 

Issue: An internal buffering error causes an incomplete query of the variants in some projects against the Variant Annotation Database in ArrayStar. The end result is that some samples in a project can be incompletely annotated with the VAD information, which could lead to erroneous results for filtering, sorting, etc.

 

Resolution: All ArrayStar users working with human variant data should update to the latest version of Lasergene. Please log in and download the most recent version of the DNASTAR Lasergene installer.

 

SeqBuilder is unresponsive when using files with partial translations

Date: 5/3/16

 

Version Affected: 13.0.0

 

Version Fixed: 13.0.2

 

Issue: SeqBuilder may become unresponsive or crash when using a file with a partial translation displayed in the sequence view.

 

Resolution: To address this issue, log in to your DNASTAR account and update your Lasergene software to version 13.0.2, which is included in the Lasergene 13.0c installer. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

SeqMan Pro may close unexpectedly when using “Force Join Contigs” function

Date: 5/3/16

 

Version Affected: 13.0.0

 

Version Fixed: 13.0.2

 

Issue: SeqMan Pro may close unexpectedly when using the “Force Join Contigs” function.

 

Resolution: This issue is fixed in Lasergene 13.0.2. To address this issue, log in to your DNASTAR account and update your Lasergene software to version 13.0.2, which is included in the Lasergene 13.0c installer. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

Targeted aligned reads are not properly reported

Date: 4/26/16

 

Version Affected: 13.0.0 

 

Version Fixed: 13.0.1/13.02 included in Lasergene 13.0c installer

 

Issue: In SeqMan NGen version 13.0.0, the number of targeted aligned reads is not properly reported due to an issue handling duplicate reads. This issue can be seen in the Enrichment Report section of the Coverage of Target Regions Report in SeqMan Pro.

 

Resolution: To address this issue, log in to your DNASTAR account and update your SeqMan NGen software to version 13.0.1, which is included in the Lasergene 13.0c installer. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

When using SeqMan NGen’s Viral-Host Integration workflow, unexpectedly few reads align to the host genome

Date: 4/7/16

 

Version Affected: 13.0

 

Version Fixed: 13.0.1

 

Issue: In SeqMan NGen v. 13.0, the Viral-Host Integration workflow may lead to an unexpectedly low number of reads aligning to the host genome. This issue has been addressed with the release of a patch, Lasergene v. 13.0.1.

 

Resolution: To address this issue, log in to your DNASTAR account and update your Lasergene software to version 13.0.1. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

When using SeqMan NGen’s transcript annotation workflow, few identified transcripts are reported

Date: 4/7/16

 

Version Affected: 13.0

 

Version Fixed: 13.0.1

 

Issue: Due to a non-optimal background parameter setting in SeqMan NGen v. 13.0, the transcript annotation workflow may produce an unexpectedly low number of identified transcripts. This issue only affects the transcript annotation (de novo Transcriptome/RNA-Seq) workflow. This issue has been addressed with the release of a patch, Lasergene v. 13.0.1.

 

Resolution: To address this issue, log in to your DNASTAR account and update your Lasergene software to version 13.0.1. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

DNASTAR no longer supports Lasergene 10, ArrayStar 5 or SeqMan NGen 4

Date: 3/1/16

 

Version Affected: Lasergene 10, ArrayStar 5, and SeqMan NGen 4 (and earlier)

 

Version Fixed: N/A

 

Issue: As of March 1, 2016, corresponding with the release of Lasergene 13.0, DNASTAR no longer supports Lasergene 10, ArrayStar 5 or SeqMan NGen 4 (or earlier).

 

Resolution: Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for assistance in upgrading to the latest version of Lasergene.

Commuter License Manager gives a “time tamper” error (Windows 10 users only)

Date: 3/1/16

 

Version Affected: 13.0

 

Version Fixed: N/A

 

Issue: Using the DNASTAR commuter license manager on Windows 10 elicits a “time tamper” error message. This message occurs due to an issue with the Sentinel licensing software used by the DNASTAR license manager. We are actively working with the Sentinel software team to resolve this issue.

 

Resolution: Until the issue is resolved, you will need to install the Lasergene commuter license manager on a different (non-Windows 10) computer, or downgrade your Windows operating system to Windows 7 or Windows 8. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for assistance.

BLAST searching fails for Lasergene versions 12.3 and earlier

Date: 3/1/16

 

Version Affected: 12.3 and earlier

 

Version Fixed: N/A

 

Issue: Sometime in 2016, NCBI will be changing its BLAST database file structure and will no longer provide the original XML format used by Lasergene version 12.3 and earlier. After NCBI implements this change, those Lasergene versions will be unable to perform a BLAST search and will instead return a non-specific error message such as: “BLAST failed to return results.” In addition (or as an alternative) to this message, a file named blast-error.txt may appear on the desktop.

 

Note that this issue will not affect Entrez database text searches, only BLAST search queries.

 

Resolution: In order to continue using Lasergene’s BLAST searching functionality, you will need to upgrade to the current version of Lasergene (13.0 or higher). Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for assistance.

SeqMan NGen no longer detects quality scores in pre-2011 Illumina data by default

Date: 3/1/16

 

Version Affected: 12.3 and earlier

 

Version Fixed: N/A

 

Issue: As of the Lasergene 13.0 release, SeqMan NGen will no longer detect quality scores in pre-2012 Illumina data by default.

 

Resolution: Starting with the Lasergene 13.0 release (March 2016), SeqMan NGen uses a standard offset for Illumina data rather than basing the offset on Illumina quality scores. If you are using pre-2012 Illumina data, you can direct SeqMan NGen to detect quality scores for those data by following these steps:

 

  1. Set up the SeqMan NGen project as desired. When you reach the Assembly Output screen, press the Save Script button. Then press the Quit button to exit from SeqMan NGen.
  2. Open the saved script in a text editor. Replace any occurrences of the words “Illumina” or “IlluminaLongReads” with either “auto” or “IlluminaQual64.” Both replacements are interchangeable. Save the edited script.
  3. Use the edited script to perform a SeqMan NGen assembly. To do this, open the Command Prompt (Win) or Terminal (Mac). Type: XNG [filepath\script name] and press Enter.

 

Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for assistance.

SeqMan Pro is incompatible with Kaspersky antivirus software (Windows users only)

Date: 10/15/2014

 

Version Affected: 12 and earlier

 

Version Fixed: 13.0

 

Issue: If Kaspersky antivirus software is installed on the same Windows computer as Lasergene, SeqMan Pro may crash when you launch or exit from it. This issue has been observed by a small number of users with Kaspersky Endpoint Security 10, but may also be an issue with other Kaspersky antivirus products.

 

Resolution: This issue was fixed in the Lasergene 13.0 release. To address this issue, log in to your DNASTAR account and download the most recent version of Lasergene. Please contact DNASTAR at 866-511-5090 or sales@dnastar.com if you need assistance.

Macintosh OS X 10.11 “El Capitan” is not compatible with Lasergene version 12.3.1 or earlier

Date: 10/13/15

 

Version Affected: 12.3.1 and earlier

 

Version Fixed: 12.3.2

 

Issue:  Macintosh released operating system OS X 10.11 “El Capitan” on 9/30/15. This operating system is incompatible with Lasergene version 12.3.1 or earlier. If you have Lasergene version 12.3.1 or earlier, updating to El Capitan will cause the loss of important Lasergene functionality, including the ability to:

 

  • Open, close and save files.
  • Run applications through the command-line (SeqMan NGen, SeqNinja).

 

Resolution: This issue is fixed in Lasergene 12.3.2, released on 10/13/15. If you download and install this version of Lasergene (or later), you may update your Macintosh system to “El Capitan” while retaining full Lasergene functionality.

 

Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for information on upgrading your applications to the latest versions.

 

 

DNASTAR no longer supports Windows XP

Date:  7/29/15

 

Version Affected:  12.3.1 and higher

 

Version Fixed:  N/A

 

Issue:  As of July 29, 2015, corresponding with the release of Lasergene 12.3.1, DNASTAR no longer supports running our software on Windows XP systems.

 

Resolution: Please contact DNASTAR at 866-511-5090 or sales@dnastar.com for assistance.

 

Unsecured network systems risk license server vulnerability

Date: 6/16/2015

 

Version Affected: DNASTAR Lasergene License Server 11.0 to 12.2

 

Version Fixed: DNASTAR Lasergene License Server 12.3

 

Issue:  A vulnerability has been discovered in the third-party license server executable (“lserv”) installed with the network version of Lasergene. If an outside party attempts to exploit this vulnerability, the user may receive unexpected error messages from lserv. This issue has only been reported for networks that do not follow recommended levels of network security.

 

Resolution:  This vulnerability was addressed with the release of DNASTAR Lasergene License Server 12.3 on July 1, 2015. To correct the issue, download and install the latest DNASTAR Lasergene License Server for Windows or Macintosh, as described in the DNASTAR Lasergene Network Setup Guide. If you need assistance, please contact DNASTAR at 866-511-5090 or support@dnastar.com.

 

After saving a help topic in PDF format, why do I see overlapping text and/or unexpected symbols?

This issue only occurs in Windows. If you see overlapping text and/or unexpected symbols after saving a Lasergene help topic as an Adobe PDF document, you may need to change your Adobe settings:

 

  1. Click Start > Devices and Printers.
  2. Double-click on Adobe PDF.
  3. Choose Printer > Properties.
  4. In the General tab, click on the Preferences button. Uncheck Rely on system fonts only; do not use document fonts. Click Apply.
  5. In the Paper/Quality tab, click on the Advanced button. Click the link Substitute with Device Font. From the drop-down menu, choose Download as SoftFont. Double-click on PostScript Options, and click the link Automatic. From the drop-down menu, select Native TrueType.
  6. Click OK, then Apply, then OK.
  7. Open the Lasergene help topic of interest and save it as an Adobe PDF document.
  8. Open the newly-saved document. The text should now display legibly.

 

The instructions above apply specifically to Windows 7, but other Windows operating systems use a similar procedure.

 

After installing Lasergene on Windows, antivirus programs may report “Shellshock” vulnerability

Date: 10/8/2014

 

Version Affected: 12.0 and higher

 

Version Fixed: N/A

 

Issue: To support MegAlign’s MAFFT alignment algorithm, the Windows version of Lasergene installs and uses a version of GNU Bash containing the recently published ShellShock vulnerability. Antivirus programs may flag this as a risk.

 

The GNU Bash installed by Lasergene is not exposed to external attackers, as it is installed for use only by MegAlign Pro. It is not used by web servers or other known attack vectors. Therefore, we believe that Lasergene installation poses no risk to our customers.

 

ShellShock vulnerability is described further on the U.S. CERT website.

 

Note: This issue does not affect Macintosh installations of Lasergene.

 

Resolution: We are actively working toward updating GNU Bash in a future release of Lasergene.

 

If desired, you may remove this version of GNU Bash from the MegAlign Pro installation. Doing so will make the MAFFT alignment engine unavailable until you perform a new Lasergene installation. For assistance in removing GNU Bash, contact DNASTAR at 866-511-5090 or support@dnastar.com.

 

A warning message that the “identity of the developer cannot be confirmed” appears when attempting installation of DNASTAR software on Macintosh OS X 10.9.5 and later

Date: 9/18/2014

 

Version Affected: 12.0 and 12.0.1

 

Version Fixed: 12.1

 

Issue: Macintosh OS X 10.9 (Mavericks) and later require a “v2” signature. Lasergene 12.0 and 12.0.1 have a “v1” signature. Therefore, when attempting to install Lasergene 12.0 or 12.0.1 or its components on Macintosh OS X 10.9.5 (or later), the following message appears: “[ApplicationName] 12.x.x Mac Install can’t be opened because the identity of the developer cannot be confirmed.”

 

Resolution:

 

To correct this issue:

 

After the release of Lasergene 12.1, please log in and download the most recent version of the software. If you need assistance, contact DNASTAR at 866-511-5090 or support@dnastar.com for help.

 

Prior to the release of Lasergene 12.1, or if you do not wish to upgrade to that version, you may circumvent the issue as follows:

 

  1. Click the OK button to close the warning.
  2. Ctrl+click on the file named [ApplicationName] 12.x.x Mac Install and select Open. You will see a warning that appears similar to the original warning.
  3. Click the Open button at the bottom of the new message.

 

The installer will now run as normal.

 

I purchased a perpetual license from DNASTAR. What rights do I have and what obligations does DNASTAR have under this license?

In the normal course of business, DNASTAR frequently grants the user of our software a perpetual license for the use of such software. A perpetual license is defined as the use of the license for the software version purchased, for an unlimited period of time. A perpetual license does not permit users to place DNASTAR’s software on more computers than were licensed for use in the initial purchase.

 

DNASTAR is not under any obligation to provide users of the software with support or additional copies of the original version of software purchased for backup, upgrades to new computers, or for any other purpose. In addition, DNASTAR is under no obligation to update its software for new computer operating systems, hardware configurations or for any other reason after initial purchase of the license by the customer. Users may continue to use a particular software version after DNASTAR support has been discontinued as long as the use of such software is not in conflict with any more recent license agreement agreed upon by the customer and only on the number of computers originally covered in the purchase agreement with DNASTAR or one of its distributors or agents.

Can DNASTAR do my assembly for me?

We’d be happy to! DNASTAR can custom assemble, analyze and deliver a finished genome, or part of a genome, along with customized visualizations and reports. In collaboration with our sister company, Scarab Genomics, we can even prepare the library, arrange for sequencing, and then assemble and analyze the resultant data.

 

For more information on any of these services, see DNASTAR’s Genome Assembly Services page.

 

How can I get help with my own specific project?

Our experienced, on-site Support team can assist you at any stage of your project by phone or e-mail. You can also request that Support set up a free, one-on-one training webinar to walk you through your project.

 

How do I reference the software in publications?

Citations for DNASTAR software should follow the format:

<Application Name with corresponding trademark>. Version <version number>. DNASTAR. Madison, WI.

For example:

SeqMan NGen®. Version 12.0. DNASTAR. Madison, WI.

To find the appropriate trademark for a DNASTAR application, please refer to the “Trademarks” section of our Legal Information page. For examples of recent publications that cited DNASTAR software, see our Published References page.

Can I publish with the free trial software?

Unfortunately, is not permissible to publish data or images obtained using DNASTAR’s free trial software. For more information, refer to the license agreement displayed during installation of the free trial software. Note that DNASTAR’s Marketing department routinely tracks citations and references to our software in the literature.

 

To purchase the software so that you can legally publish data and images (including those generated while you were using the free trial version), choose either of the following options:

 

  • Contact our Sales and Support staff by e-mailing support@dnastar.com or by calling 866-511-5090 in the U.S. and Canada. For European and UK contact numbers, please see our Contact Us page.

How can I see which version is currently released and which version I’m running?

To see which version number is the most current, see our Product Updates page.

 

To learn which version of an application you are running:

 

  1. Launch the DNASTAR application.
  2.  Select Help > About [AppName] on Windows, or [AppName] > About [AppName] on Macintosh to open a pop-up window showing the version number of the application.

How can I tell which DNASTAR products I own?

To see a list of DNASTAR products that you have purchased:

 

  1. Go to the DNASTAR log in page.
  2. Enter your Email/User ID and Password to log into your account.

 

You will be taken to a page listing your purchased applications and their version numbers, along with the number of remaining keys and the expiration dates for service plans.

 

An informal way to see which products have been installed/authorized is to launch the DNASTAR Navigator application. Applications listed in color are installed/authorized, and those that are “grayed out” are not. Note that this procedure does not differentiate between purchased versions of the applications and free trial versions. If you have installed a free trial version, it is best to use the numbered steps, above.

Templated assembly fails when using certain reference sequences or genome templates

Date:   7/28/2014

 

Version Affected:  12.0 and earlier

 

Version Fixed:  12.0.1

 

Issue:  Rarely, specific reference sequences or genome templates may cause SeqMan NGen to crash during the assembly phase.

 

Resolution:   Crashes have been reported to occur when using particular GenBank (*.gbk) or General Feature Format (*.gff) files, and for the Arabidopsis 138 template. However, it may also occur for other file types or genome templates.

 

This issue was fixed in 12.0.1. If you are experiencing this problem, please request a download link by contacting DNASTAR Support at 866-511-5090 or support@dnastar.com.

 

Clustal Omega alignment does not complete and results in a “fatal error” message

Date:   6/17/2014

 

Version Affected:  11.2 and higher

 

Version Fixed:  N/A

 

Issue:  Clustal Omega requires that each sequence in an alignment contain at least one residue that is not an ambiguity code.

 

Resolution:

 

  • DNA sequences must contain at least one A, C, T or G.
  • RNA sequences must contain at least one A, C, U, or G.
  • Protein sequences must contain at least one A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W or Y.

 

If there are any sequences that do not meet this requirement, Clustal Omega will terminate with a “fatal error” message (visible in the MegAlign Pro Console), and no alignment will be created.

 

To address this issue, you can do either of the following:

 

  • Remove the sequence and try aligning again with Clustal Omega.
  • Include the sequence, but switch to MAFFT or MUSCLE as the alignment method. Neither of these algorithms requires sequences to contain at least one non-ambiguous residue.

 

If you have any questions about this issue, please contact DNASTAR by calling 866-511-5090 or by e-mailing us at support@dnastar.com.

 

MUSCLE gives similar, but not identical, alignment results on Windows and Macintosh

Date:   4/20/2013

 

Version Affected:  11.0 and later

 

Version Fixed:  N/A

 

Issue:  Performing an identical MUSCLE alignment on the two platforms yields correct results on both platforms, but the results may not be identical to one another.

 

Resolution: This discrepancy may be due to a slight difference in the number of iterations used during assembly.

 

While performing a SeqMan NGen assembly on the DNASTAR Cloud Virtual Desktop, the virtual desktop suddenly shuts down

Date: 4/20/2013

 

Version Affected:  11.0 and later

 

Version Fixed:  N/A

 

Issue: When a SeqMan NGen assembly uses all available memory, the connection to the DNASTAR Cloud may be lost without warning.

 

Resolution:   This has been observed on Safari and Google Chrome browsers, but may affect other browser types as well. If this issue occurs, you will lose your connection and receive an error message telling you that the connection was lost. If you click on the Abort button provided, you will be taken to the DNASTAR – My Licenses page. You should now be able to re-connect to the virtual desktop in the usual way. (See DNASTAR Cloud Virtual Desktop Help for details).

 

In window headers, MegAlign may designate MUSCLE-aligned (.msf) files from MegAlign Pro as “ClustalW” or “ClustalV”

Date:   4/20/2013

 

Version Affected:  11.0 and later

 

Version Fixed:  N/A

 

Issue:    When a MUSCLE-aligned (.msf) file from MegAlign Pro is opened in MegAlign (or sent directly to MegAlign) and a View Menu command is used, the resulting window contains the word “ClustalV” or “ClustalW” as part of its heading.

 

Resolution: The original MUSCLE alignment is actually unaltered, and the Clustal algorithm is never invoked. Only the label at the top of the window is incorrect.

 

ArrayStar projects may not be compatible with earlier versions of ArrayStar

Date: 3/15/12

 

Version Affected:  All currently supported versions

 

Version Fixed:  N/A

 

Issue:  Once certain changes have been made to an ArrayStar project in one major release version (e.g., version 13.x), you may not be able to open the file in any version of ArrayStar with a lower number to the left of the decimal (e.g., version 12.1). This is not an issue within a major release. For example, you could edit a project in version 12.1 and then open it successfully in version 12.0.

 

Resolution: If you plan to edit a file but later open it in an earlier major release version of ArrayStar, we recommend saving a copy of the file prior to editing. If you have questions, please contact DNASTAR at 866-511-5090 or sales@dnastar.com.

 

 

View Genomics Quick Tips
 
View Structural Biology Quick Tips
 
View All Lasergene Quick Tips

Leave a Reply

Your email address will not be published. Required fields are marked *

You may use these HTML tags and attributes: <a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <strike> <strong>

Current ye@r *