Add the app to Matlab, and design the oligos based on the below instructions:
a) Design fragment-related oligos: Input name and sequence of fragment (>= 35 bp), and click button “Click to design oligos for FRAGMENT”. Remember to include the conversed G and T in the input sequence. If the fragment lenght is longer than 91 bp, Foligos with or without PS-bonds will be designed and displayed on the right-side of the window. If the fragment length is < 91 bp, Noligos (Non-modified fragment oligos) will be designed and displayed in addition to Foligos. Users can use button “Copy oligo info” to copy information of the designed oligos to clipboard of the desktop's operating system (so far only Microsoft Windows 10 has been tested), which can be pasted into a spreadsheet of Microsoft Excel. The software arranges the oligo information according to format requirement of the IDT ordering system, and it determines the synthesis scale automatically. Click button “Clear results” to reset the software for the for next design.
b) Design barcode-related oligos: Input name and sequence of barcode (20-80 bp) based on the instruction, and click button “Click to design oligos for BARCODE”. Two types of Boligos and Aoligos will be designed, and the oligo information will be displayed. The software automatically determines sticky end (SE) sequence. If it cannot find a suitble SE sequence, user can consider to extend the barcode sequence to enlarge the search space. User can manually specify the SE sequence to overwrite the SE search step but it may result in lower assembly efficiency. Boligos designed here can be used with CLIVA, Gibson and In-fusion assembly method. Aoligos designed here are for the CLIVA method. User may manually modify the designed Aoligos for Gibson and In-fusion method: remove the PS modifications and extend SE sequence to meet requirement of those methods. This version of the software does not support restriction enzyme based cloning and we will release new version to support them.
Kang Zhou Group at NUS (2019). Oligo Designer for GT Standard (https://www.mathworks.com/matlabcentral/fileexchange/71880-oligo-designer-for-gt-standard), MATLAB Central File Exchange. Retrieved .
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