A gene sequence file can be created by inputting a DNA sequence, importing a file, or selecting from an existing plasmid library if available in the project. Gene sequences are composed of the four nucleotides (A, T, C, G) arranged to encode genetic information, typically including exons and introns. A plasmid often contains multiple functional elements. By analyzing sequence data, users can identify functional regions and perform molecular experiments.
Creating a New Sequence File
Step 1: Log into ZettaLab and navigate to Molecular Tools.
Step 2: Select Gene Sequence.
Step 3: Click Create New File.
Step 4: Complete metadata fields, including Project, Storage Folder, and File Name.
Step 5: Paste the DNA sequence into the input box and select the topology (linear/circular) based on sequence properties.
Step 6: Click Confirm to generate the gene sequence file.
Importing a Gene Sequence File
Sequence files downloaded from databases (e.g., FASTA format) often contain annotations and features requiring specialized tools for processing.
Step 1: Log into ZettaLab and navigate to Molecular Tools.
Step 2: Select Gene Sequence.
Step 3: Click Import File.
Step 4: Fill in metadata fields.
Step 5: Upload the file via drag-and-drop or manual selection.
Step 6: Click Confirm to generate the gene sequence file.
Selecting from Plasmid Library
ZettaLab hosts thousands of pre-annotated plasmid maps. Users can search by name or select from shared project libraries.
Step 1: Log into ZettaLab and navigate to Molecular Tools.
Step 2: Select Gene Sequence.
Step 3: Click Select from Plasmid Library.
Step 4: Choose the source plasmid library.
Step 5: Locate the target plasmid, click Copy to Project, enter metadata, and confirm.
Creating a Primer
Primers are short synthetic DNA fragments (18-30 bp) critical for PCR and related experiments. Effective primers require optimized GC content and annealing temperature (typically 58-60°C).
Step 1: Open the target gene sequence file.
Step 2: Define the amplification region.
Step 3: Select primer binding sites at both ends of the target region, adhering to primer design principles.
Step 4: Right-click and select Create > Primer.
Step 5: Assign a primer name.
Step 6: Designate upstream/downstream orientation (downstream primers require reverse complement sequences).
Step 7: Click Confirm.
Automated Primer Design
For high-throughput workflows, ZettaLab offers automated primer design for Gibson Assembly and PCR amplification.
Step 1: Navigate to Automated Primer Design under Molecular Tools.
Step 2: Select the primer application scenario (e.g., Gibson Assembly, PCR).
Step 3: Choose the source project and gene sequence file.
Step 4: Set parameters: length (18-27 bp), annealing temperature (58-60°C), GC content (40-60%).
Step 5: Select the amplification region on the sequence or plasmid map.
Step 6: Click Start Design to retrieve primer sequences and product details.
Molecular Cloning
ZettaLab enables in silico validation of multi-fragment cloning workflows, predicting ligation feasibility and product sequences.
Step 1: Navigate to Molecular Cloning under Molecular Tools.
Step 2: Select the cloning scenario.
Step 3: Choose the source project and vector sequence.
Step 4: Add insert fragments from plasmid libraries.
Step 5: Specify linearization methods, enzymes, and retention regions for each fragment.
Step 6: Repeat Steps 5-8 for additional fragments.
Step 7: Click Simulate to visualize ligation results.
Sequence Alignment
ZettaLab employs proprietary algorithms for efficient and accurate sequence alignment, supporting applications such as clone validation, knockout efficiency analysis, and homology detection.
Step 1: Navigate to Sequence Alignment under Molecular Tools.
Step 2: Select the source project and sequences for alignment.
Step 3: Adjust sequence order (top sequence serves as reference).
Step 4: Click Start Alignment.
Step 5: Save results via the top-right menu.
Shared Libraries
Project members can collaboratively manage validated biological components (plasmids, enzymes, primers, features) through shared libraries.
Step 1: Categorize components (plasmid/enzyme/primer/feature).
Step 2: Select the target library and enable sharing permissions.
Step 3: Create a new group within the library.
Step 4: Name the group and import/add components.
Electronic Laboratory Notebook (ELN)
Creating and Editing ELN
An ELN digitizes experimental documentation, supporting text, figures, hyperlinks, and integration with lab software for enhanced traceability.
Step 1: Click New Experiment Record.
Step 2: Assign project, folder, and file name.
Step 3: Edit content.
Step 4: Save via the top-right menu.
Saving and Sharing ELN Templates
Step 1: Complete an ELN entry.
Step 2: Click Save as Template.
Step 3: Access templates via the Template Library.
Step 4: Convert to a team template for project-wide visibility.
Using and Modifying Templates
Step 1: Navigate to Experiment Record Templates.
Step 2: Select and preview the desired template.
Step 3: Click Use Template to create a new ELN.
Step 4: Edit private templates via My Templates.
Exporting ELN as PDF
Step 1: Open the target ELN entry.
Step 2: Click Export as PDF.
Step 3: Save or print the PDF.
ELN Annotation Tool
Step 1: Highlight the target text/region.
Step 2: Click the Annotation icon.
Step 3: Add comments in the sidebar. Annotations trigger user notifications.
ELN Cross-Referencing
Step 1: Place the cursor at the target location.
Step 2: Type "@" to reference files, users, or experimental data.
ELN Content Insertion
Step 1: Place the cursor at the target location.
Step 2: Type "/" to insert files, tables, timestamps, or graphical elements.
ELN Headers and Numbering
Step 1: Select the target header.
Step 2: Assign header levels via the "+" menu.
Step 3: Apply ordered/unordered lists using the toolbar.
Collaboration Features
Project File Management: Organize files hierarchically.
Member Management: Add/remove members and adjust permissions.
Permission Settings: Configure visibility/editing rights based on project sensitivity (e.g., IP-related research).