Server at Davidson College
The DIY Oligator allows you to determine possible oligonucleotide sequences when the Oligator cannot find a satisfactory set, or when you want to specify particular oligos. An optimal set of oligos have similar melting temperatures. Melting temperature depends on the G-C count and total length of the oligo. Therefore, sequences with approximately equal G-C counts will have similar melting temperatures.
To begin, enter the DNA or RNA sequence as seen below. As you enter your sequence it should be displayed below the input box.
Step 2 provides a tool for determining how many G's and C's should be in each overlap. Select a number of overlaps and the number of G's and C's that should be in each oligo is displayed below. If the number of overlaps is less than seven, an image will appear that shows the overlaps and oligos.
Next, starting from the beginning of the sequence, enter the bases until the number of C's and G's in the sequence is the desired number as determined in step 2. The letters will be highlighted in the remaining sequence as you type. Then click "Submit Overlap." The oligo will be replaced with a horizontal line in the remaining sequence.
Continue this process until the entire sequence has been submitted. At this point the remaining sequence should contain no bases and therefore the remaining sequence is a line.
Now enter a project name and click "Generate Oligos." If no name is entered, "oligo" will be the name of the project.