How to use DNA Baser
Part 3

How to assemble using a reference sequence

 





Level: beginner

     This tutorial will show you how to assemble contigs using reference sequence files.

     DNA Baser uses the reference sequence to:
                                         - give the contig orientation
                                         - crop the contig
     The reference sequence is not used for calculating the consensus sequence of the contig.

1. Open DNA Baser by clicking its icon on your desktop. When DNA Baser starts, the Project Manager should be opened by default. Navigate to the folder where your files are.

2. Choose a name for this current project. DNA Baser will automatically choose a name for you but you can change it. Use this box to choose/change project's name:

3. Next step is to choose a reference sequence. Drag and drop the desired sequence file in this panel: .
The check box must be activated in order to assemble using a reference sequence.

4. Select the two or more files that are going to be assembled by adding them to the JOB LIST. DNA Baser supports SCF, ABI, FASTA and SEQ.

You can add files to the Job List in several ways:

-use the button to add selected file/files to the Job List.
-use the button to add all files to the Job List.
-using your mouse, drag and drop files one by one from File List to the Job List.
If you want to remove files from the Job List, than use button.
5. The final step is to press the START button. In this moment, DNA Baser should begin the assembling process.

If something is wrong, the START button will be disabled:
This can be caused by:
-less than 2 files in the Job List
-invalid combinations of file types in the Job List
-one or more files in the Job List are invalid or it has been removed from your computer's hard disk meanwhile.
6. After the assembly process, you can check the log file. If DNA Baser has not already opened the log window for you, then press this button to display it.

7. The reference sequence will be placed in the contig grid (click here to read more about the contig grid) on the first position and it will have a light-pink background.

Read the next tutorial to find out how to assemble using the batch mode. If you have any questions, don't hesitate to write an email to us or to use our forum for support.