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DNAMAN:Questions and Answers

latest update:2020/10/05 Views:951
I used DNAMAN for my research project. How do I acknowledge in my publications?

Questions and Answers

 

I used DNAMAN for my research project. How do I acknowledge in my publications?

We highly appreciate your citations of the DNAMAN sequence analysis software. Please take a look how DNAMAN is acknowledged in peer-reviewed journals.

 

What is Home & Student license? May I purchase this version instead of single user licence?

DNAMAN Home & Student license is for students (including Graduates, PhDs and PostDocs) who wish to use the program for school or home projects related to molecular biology and bioinformatics. The Home & Student version offers the same functionalities as other versions of DNAMAN. You may not purchase this version if you intend to use DNAMAN to advance your research projects of academic or industrial applications.

 

Where should I ask questions about the DNAMAN program?

Fill out a form in Technical Support page.

 

How do I manually update DNAMAN for Windows?

Use Windows Explorer to browse DNAMAN program folder (usually C:\Program Files (X86)\DNAMAN). Find the file LBUpdate.exe and right click it. Windows will show a context menu and choose "Run as Administrator". DNAMAN will check for available updates from Lynnon website and update itself to the latest release of your licensed version.

 

How do I manually update DNAMAN for OSX?

Open an Terminal window and issue the command: sudo /Applications/DNAMAN/lcupdate . You will be asked for password and enter it. DNAMAN will check for available updates from Lynnon website and update itself to the latest release of your licensed version.

 

I have downloaded the DNAMAN Demo file. Now what do I do next?

Locate the downloaded file (usually in Downloads folder) and double-click it to start program installation. Follow the on-screen instructions to complete the setup.

 

I was asked for Username and Serial Number during installation of the DNAMAN Demo program.

Check "Setup as Demo" option and do not enter information in the fields of Username and Serial Number.

 

DNAMAN shows evaluation period is expired. What should I do to continue using the software?

DNAMAN demo version has a trial period of 45 days upon installation. You may not be able to use DNAMAN demo version beyond the free trial period. Re-installation of demo version will not extend the trial period. Should you wish to continue using DNAMAN, please contact Lynnon Biosoft to purchase an appropriate license.

 

I have installed the DNAMAN program on my computer, but I do not know how to work with it.

If you use DNAMAN for the first time, you may follow the instructions described below.

To perform sequence analysis:

i. Choose the File | Open menu.

ii. Select the Example1 file from Open File dialog box. Click the Open button.

iii. Choose the Restriction | Restriction Analysis menu to perform restriction analysis on Example1.

iv. After restriction analysis, choose the Protein | Translation menu to translate Example1 to amino acid sequence.

 

To draw a restriction map without sequence:

Choose the Restriction | Draw Map menu. A plasmid map is drawn in a restriction map window. Double-click on the window to display the map properties and make modification.

 

Tips: All objects in a restriction map can be moved around by drag-and-drop. Restriction sites and Text objects can be aligned when they are selected.

 

What is the largest sequence DNAMAN can handle?

In theory, DNAMAN can work with sequences up to 2 giga-bases(2x109). The real limitation is the computer power and resources. We have tested the program with sequences of 10 megabases for restriction analysis and sequence searches. The functions of multiple alignment and sequence assembly have different limitations in sequence handling.

 

What are the limitations of multiple alignment?

You may use up to 32000 sequences with a maximum length of 64000 bases. Again, the limitation is the computer power and resources. We have successfully aligned 1000 sequences of approximately 300 amino acids with the program.

 

What are the limitations of sequence assembly?

You may use up to 32000 DNA fragments with a maximum length of one giga-bases. Again, the limitation is the computer power and resources. We have successfully assembled 5000 sequences of approximately 2000 bases with the program.

 

What are the major differences between Windows and OSX DNAMAN versions?

DNAMAN for Windows has an integrated Web browser and the Mac OSX version does not. DNAMAN for Windows includes a drawing program, LBDraw, but the Mac OSX version does not.

 

May I use other programs within DNAMAN?

Yes, you may. Use the File | Run menu to launch a program. There is an option to display the results in the DNAMAN Desktop.

 

What is the DNAMAN browser for? May I use my favorite browser, instead of the integrated one?

The DNAMAN browser is designed to browser sequences and databases on the Internet or your Intranet, and use them directly for analysis. You have an option to use your favorite browser by choosing the Info | Settings menu.

 

Which functions of DNAMAN are multiple threaded and why?

Multiple threaded functions divide heavy computing tasks to run in paralelle. The multiple alignment of DNAMAN is multiple threaded. You may launch up to 16 processes of multiple alignment running in the same time. The sequence assembly function is also threaded. Producing trees from multiple alignment falls also into this category.

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