Performing an Assembly of DNA Fragments using Sequencher

1. Once Sequencher has been downloaded and uncompressed, the program may be installed by double-clicking on the "Sequencher Demo Installer" desktop icon. This creates a Sequencher Demo folder on your hard disk. Within this folder, click on "Sequencher 3.0.1 Demo" to start up the program.

2. When Sequencher starts up, the assembly window will appear. You are now ready to import the data files you have downloaded and assemble them.

3. To import student data, choose File->Import->Folder of Sequences. Select the folder which contains the data of interest, and choose "OK."  

4. Sequencher will then prompt you to make sure you wish to import the entire folder. Choose "Import All Files in Folder." Each student data file will be imported into the Sequencher window.

5. If they are not already selected, select the files to be assembled. The selected files will appear in blue.

6. To start the assembly process, simply click on "Assemble Automatically." It may take some time for your computer to complete the analysis. Once it is finished, you will see files in the analysis window with names starting with "Contig." Each contig file contains an assembly of overlapping DNA fragments. A contig may be viewed by double-clicking on the small icon to the left of the contig file name.

7. When you open a contig, Sequencher will display the "overview window," which shows which overlapping fragments were assembled into the contig. Each horizontal line represents one student membrane or automated DNA sequence.

8. Important features of the sequence are marked by red and green symbols. A legend appears at the bottom of the window to assist you in interpreting your data.

9. By clicking on the "bases" button in the upper left hand corner, a different view appears showing the raw sequences of each fragment making up the contig. It is here where editing of the final sequence is performed.

10. Students may wish to take the DNA sequence data they have read from the downloaded membrane images and insert it into the assembly window to see where their data fits in relation to the rest of the students' sequences. Students should type their sequence into a word processor, save as a text file, then import this file following the directions given above for importing sequences. After assembly is performed, students can then search the various contigs for their fragment.

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Virtual DNA Sequencing Overview