The Melting Temperature Window
The Tm Graph Window is the core window of the OLIGO program. It is automatically displayed when DNA sequence is loaded, and includes the following displays, functions, and capabilities in the default configuration:
• A close-up of approximately 90 nucleotides of the active sequence at the bottom of the window, both the positive strand (in red) and the negative strand (in blue). This display can be zoomed-out using the Zoom .
• A Tm graph of the displayed sequence segment, calculated using the nearest neighbor method. Each point or bar on the graph represents the Tm of an oligonucleotide, the 5'-terminus of which is located at that position. The Tm is calculated for an oligonucleotide length that is set in the "Current Oligo Length" option from the Change menu &emdash; the default is a 21-mer. The set oligo length is displayed on the window title bar.
• Cursor and cross hairs. The Tm window includes a mouse-driven "finger-pointer" cursor.
• The protein sequence translated from the DNA/RNA active sequence in the selected reading frame (set in Change &emdash; Display Parameters). The display of the protein sequence is optional and may be changed using the internal window menu, displayed just above the graph.
• The mean Tm of all the oligonucleotides of the selected length in the active sequence &emdash; the center horizontal dotted line on the graph. (Display is optional.)
• The Upper and Lower Tm selection limits as currently set for the searches &emdash; the upper and lower horizontal dotted lines on the graph. (Display is optional.)
• The Upper and Lower Primer selection buttons and other control icons for the "Melting Temperature" window.
• The Current Oligo &emdash; the oligonucleotide sequence underlined and in upper case letters within the active sequence. The positive and negative strand sequences are both part of the Current Oligo. The Current Oligo is always present in the "Melting Temperature" window and advances across the active sequence.
• The Upper and/or Lower Primer, when selected and located within the "Melting Temperature" window subsequence. The Upper Primer is displayed in red one line above the positive strand of the active sequence and includes a primer extension arrow. It is displayed in upper case letters except for nucleotides within the Upper Primer mismatched to the active sequence. These are displayed in lower case letters. The Lower Primer is displayed in blue one line below the negative strand of the active sequence and has the same characteristics as the Upper Primer.
By default, the "Melting Temperature" window displays the Tm plot of every 21-mer of the active sequences. However, there are two other display modes &emdash; DG values, %GC composition, or, for degenerate sequences, it may display degeneracy. You can change the display from the Graph sub-menu.