Table of Contents
Sequence View
- The sequence view allows you to see the details of the design sequence.
The Sequence Navigation Windows
- There are two movable windows to allow navigation through through the sequence:
The Global Sequence Window
- The global sequence window (label in screenshot 3) allows selection of a large area of the construct
- In a circular construct, the global window can straddle the origin.
- The size of the global window can be altered by dragging one of the open squares at its boundary (label in screenshot 3).
- The location of the global window can be altered by:
- clicking anywhere within the selected part of the sector and dragging it.
- clicking anywhere on the construct: the click point will become the center of the window.
The Local Sequence Window
- The local sequence window (label in screenshot 3) allows base-by-base navigation through the sequence
- The local window can be moved in the same way as the global window.
- The sequence within the local window is displayed (label in screenshot 3).
The Sequence Display
- At the top of the sequence display, the sequence of the final construct is shown.
- Below the construct sequence is a grid where oligonucleotides are created and displayed.
- Below the oligonucleotide grid, the sequence of each element is displayed in a sequence bar. Above the sequence bar is the name for that element and an arrow denoting its orienation.
- The sequences for DNA elements and amino acid elements are displayed differently:
Display of Amino Acid element sequence
- The amino acid sequence bar shows the amino acid sequence of the element
- Beneath each amino acid, each of the codons encoding that amino acid are displayed
- The codons are shown in the order of their frequencies in the codon table selected for the construct
- The highest frequency codon is at the top
- The codon that is currently selected to encode each amino acid is colored
- Codons whose frequencies are higher than the threshold frequency are colored green.
- Codons whose frequencies are lower than the threshold frequency are colored yellow.
- The threshold frequency can be changed in the Details View
- A new codon may be selected to encode any amino acid by clicking on a different codon button.
- The new choice changes the sequence displayed for the final construct.
- The new choice changes the sequence of any oligonucleotide that overlaps the change.
- Clicking on the codon that is already selected will clear that codon choice and leave a gap in the final construct sequence.
- For amino acid elements that are in the reverse direction, the codons are shown in the forward direction beneath the amino acid
- underneath a methionine in a reverse direction amino acid element the codon is displayed as ATG
- the sequence of the final construct above the methionine is shown correctly as CAT
Display of DNA element sequence
- The DNA sequence bar shows the DNA sequence of the element
- Beneath each triplet, each encoded amino acid is displayed
- There are 6 different amino acid sequences shown, 3 in the forward reading frames and 3 in the reverse.
- The amino acid one letter code is shown in line with the middle nucleotide of the codon.
- The direction of the reading frame is indicated by a faint arrow.
- If a DNA element is adjacent to an amino acid element, the reading frame that is in the same frame as the amino acid element will be colored to match that element.
Editing Sequence Elements within the Sequence View
- The sequence of individual elements within the final construct can be edited in the Sequence View.