Table 2.

Additional software features. These additional features are available from various locations, including drop-down menus, the Property panel and the Context menu.

Additional feature	Details
Supported file types	Genebank DNA sequence (.gb), Sequence text file (.txt), Sequence file (.seq), Sequencing result (.ab1,. scf). MCDS DNA file (.vct), MCDS project (.vxt)
Sequence import	Load sequence with the “Load Sequence” button
	Copy sequence files (.gb .txt .seq .ab1.scf) in Windows file explorer and paste into MCDS flowchart view
Restriction enzymes	Restriction enzymes can be managed and customized in “Restriction Enzymes” button in the “Settings” menu
Recombination sites	Recombination sites can be managed and customized in “Recombination Sites” button in the “Setting” menu
gRNA Sites	gRNA sites can be managed and customized in “gRNA Sites” button in the “Setting” menu.
Codon table	MCDS can download all genes of an organism from KEGG and calculate codon usage.
	Selected codon table is used in “Translation” and “Codon optimization”
Digestion buffers	MCDS manages digestion buffers by supplier and product name so as to describe the difference between buffers and commercial names (e.g. buffer specificities of BcuI from Thermofisher and SpeI/SpeI-HF from NEB can be all stored in MCDS)
	MCDS stores the buffer activity table and can automatically calculate the optimal buffer for a combination of enzymes
Feature setting	All features found in genebank files, vector (vct) files and pasted files (when copied from one node to another, or Windows Explorer) will be automatically included in the project.
	In all DNA generated in MCDS, features will be automatically annotated
	Features can be managed and edited in “Manage Features” of the dashboard
Enzyme setting	User can type or select enzymes in the dashboard, and all enzyme sites will be shown in all the vector maps
Node status	Users can specify the status of a node: “Not Started”, “In Progress”, “Finished” or “Obsolete”. Node background will be changed to a corresponding color to present the status of node in the flowchart
Sequencing data	Users can embed sequence result files into the “Sequencing Results” of a node and data traces can be displayed. Embedded files can be exported
Figure file	Users can embed images such as gel figures into the “Gel Figures” tab. Embedded files can be exported
Primer management	MCDS can maintain a list of primers. In the project summary, MCDS detects recorded primers so that users can only send newly designed primers into clipboard
Primer designer	Primer Search: users can first select a region in the sequence viewer or vector map and then click “Find” to search for a pair of primers with Tm above given value and with minimal hairpins, dimers, cross dimers to amplify the selected region. Additional candidates are listed in the drop button of the “Find” button
	One click primer design: users can click the row above or below the double-strand sequence in the sequence viewer to design a primer with 5′ end starting at the clicked nucleotide and with Tm above give value
	Gibbs free energy change values and affected nucleotides are shown for hairpins, dimers, cross dimers and priming sites
Ligation and recombination algorithms	Ligation and recombination are the same algorithm with different “Connection” and “Cyclization” methods
	Supported recombination: Lambda red recombination, homologous, Gibson assembly
	Normal mode: users can specify how many rounds the algorithm should be applied to the substrates
	Exhaustive mode: users can specify how many copies of each fragment should be used in the assembly. The algorithm will try to find all possible products that use up all given fragments
Online database	This function can be accessed from the button or main menu. Users can search and download DNA sequence from KEGG and NCBI in MCDS. Obtained sequences will be added to the flowchart as nodes
Node status tracking	Users can specify the status of a node as “Not Started”, “In Progress”, “Finished” or “Obsolete”. The status of a node is shown by its background color (white, red, green or gray)
Group copy and group paste	Group Copy and Group Paste can be accessed from “Copy Group” and “Paste Group” buttons or context menu. Group Copy copies all selected nodes with their relations in the flowchart. Group Paste pastes the copied nodes and relation into a flowchart and automatically load the features in nodes if the features are not yet included in the project
ORF detection	ORF detection can be accessed using the Context menu by right-clicking when one or more nodes are selected. It detects all ORFs that meets the specified conditions and will draw them in the node. Features that are not recorded in the feature setting (including any unsaved ORFs in the previous detection) will be removed during the ORF detection.
	In order to save the detected ORFs to the feature setting, the detected ORFs of interest must be managed in a sequence viewer of the Property panel.