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Introduction to CLC Main Workbench
- Contact information and citation
- System requirements
- Installation and startup
- Workbench Licenses
- Plugins
- Network configuration
User interface
- View Area
- Zoom functionality in the View Area
- Toolbox panel
- Processes tab and Status bar
- Element Info view
- History view
- Workspace
- List of shortcuts
Data management and search
- Navigation Area
- Working with non-CLC format files
- Customized attributes on data locations
- Searching for data in CLC Locations
  - Quick Search
  - Local Search
- Backing up data from the CLC Workbench
- Working with AWS S3 using the Remote Files tab
User preferences and settings
- General preferences
- View preferences
- Data preferences
- Advanced preferences
- Export/import of preferences
- Side Panel view settings
Printing
- Selecting which part of the view to print
- Page setup
- Print preview
Connections to other systems
- CLC Server connection
  - CLC Server data import and export
- AWS Connections
- Public S3 buckets
Importing data
- Standard import
Exporting data and graphics
- Data export
- Export graphics to files
  - File formats
- Export graph data points to a file
- Copying and pasting data from an open view
Working with tables
- Table view settings and column ordering
- Filtering tables
  - Simple filtering
  - Advanced filtering
Data download
- Search for Sequences at NCBI
  - NCBI search options
  - Handling of NCBI search results
- Search for PDB Structures at NCBI
- Search for Sequences in UniProt (Swiss-Prot/TrEMBL)
  - UniProt search options
  - Handling of UniProt search results
- Sequence web info
Running tools, handling results and batching
- Running tools
  - Running a tool on a CLC Server
- Handling results
- Batch processing
Metadata
- Creating metadata tables
  - Importing metadata
  - Creating a metadata table directly in the Workbench
- Associating data elements with metadata
  - Associate Data Automatically
  - Associate Data with Row
- Working with data and metadata
- Moving, copying and exporting metadata
Workflows
- Creating and editing workflows
- Workflow elements
- Launching workflows individually and in batches
- Advanced workflow batching
  - Batching workflows with more than one input changing per run
  - Multiple levels of batching
- Template workflows
  - Trim and Map Sanger Sequences
- Managing workflows
Viewing and editing sequences
- Working with sequences
- Working with sequence lists
- Working with annotations
- Sequence element information
- View as text
3D Molecule Viewer
- Importing molecule structure files
- Viewing molecular structures in 3D
- Customizing the visualization
  - Visualization styles and colors
  - Project settings
- Tools for linking sequence and structure
- Align Protein Structure
  - Example: alignment of calmodulin
  - The Align Protein Structure algorithm
- Generate Biomolecule
Sequence alignment
- Create an alignment
- View alignments
  - Bioinformatics explained: Sequence logo
- Edit alignments
  - Realignment
- Join alignments
- Pairwise comparison
  - The pairwise comparison table
- Bioinformatics explained: Multiple alignments
Phylogenetic trees
- Tools for tree construction
- Tree Settings
- Additional tree views
  - Tree table view
- Bioinformatics explained
General sequence analyses
- Annotate with GFF/GTF/GVF files
- Create Complexity Plot
- Create Dot Plot
- Create Sequence Statistics
  - Bioinformatics explained: Protein statistics
- Extract Sequences
- Join Sequences
- Pattern Discovery
- Shuffle Sequence
- Motif
Nucleotide analyses
- Convert DNA to RNA
- Convert RNA to DNA
- Reverse complements of sequences
- Translation of DNA or RNA to protein
- Find open reading frames
Protein analyses
- Protein charge
- Antigenicity
- Hydrophobicity
  - Hydrophobicity graphs along sequence
  - Bioinformatics explained: Protein hydrophobicity
- Download Pfam Database
- Pfam domain search
- Download 3D Protein Structure Database
- Find and Model Structure
  - Create structure model
  - Model structure
- Secondary structure prediction
- Protein report
- Reverse translation from protein into DNA
  - Bioinformatics explained: Reverse translation
- Proteolytic cleavage detection
  - Bioinformatics explained: Proteolytic cleavage
Sequencing data analyses and Assembly
- Importing and viewing trace data
  - Trace settings in the Side Panel
- Trim sequences
  - Trimming using the Trim Sequences tool
  - Manual trimming
- Assemble sequences
- Assemble sequences to reference
- Sort sequences by name
- Add sequences to an existing contig
- View and edit contigs and read mappings
- Reassemble contig
- Secondary peak calling
- Extract Consensus Sequence
Primers and probes
- Primer design - an introduction
- Setting parameters for primers and probes
- Graphical display of primer information
  - Compact information mode
  - Detailed information mode
- Output from primer design
- Standard PCR
- Nested PCR
- TaqMan
- Sequencing primers
- Alignment-based primer and probe design
- Analyze primer properties
- Find binding sites and create fragments
  - Results - binding sites and fragments
- Order primers
Cloning and restriction sites
- Create Sequence Constructs
  - Create Sequence Constructs output
- Homology Based Cloning
- Gateway cloning
- Restriction Analysis and Cloning
- Gel electrophoresis
  - Gel view
RNA structure
- RNA secondary structure prediction
- View and edit secondary structures
- Evaluate structure hypothesis
  - Selecting sequences for evaluation
  - Probabilities
- Structure scanning plot
  - Selecting sequences for scanning
  - The structure scanning result
- Bioinformatics explained: RNA structure prediction by minimum free energy minimization
  - The algorithm
  - Structure elements and their energy contribution
Expression analysis
- Experimental design
- Transformation and normalization
- Quality control
- Feature clustering
  - Hierarchical clustering of features
  - K-means/medoids clustering
- Statistical analysis - identifying differential expression
- Annotation tests
  - Hypergeometric Tests on Annotations
  - Gene Set Enrichment Analysis
- General plots
BLAST search
- BLAST against local data
- BLAST at NCBI
- Output from BLAST searches
- Local BLAST databases
- Manage BLAST databases
- Bioinformatics explained: BLAST
Utility tools
- Extraction
  - Extract Annotated Regions
- Filtering
  - Filter Based on Name
  - Filter on Custom Criteria
- Renaming
  - Rename Elements
  - Rename Sequences in Lists
- Reports
- Sequences
Appendix
- Graph preferences
- Proteolytic cleavage enzymes
- Restriction enzymes database configuration
- Technical information about modifying Gateway cloning sites
- IUPAC codes for amino acids
- IUPAC codes for nucleotides
- Formats for import and export
  - List of bioinformatic data formats
  - List of graphics data formats
- Gene expression annotation files and microarray data formats
- Custom codon frequency tables
- Matrices for alignment calculation
Bibliography

Safe mode

When troubleshooting, it can on occasion be helpful to start the Workbench in safe mode. To do this, press and hold down the Shift key while the program starts up.

When starting in safe mode, user settings are deleted. User settings include information such as Side Panel settings, refresh tokens for QDI Licensing sessions, previously used settings, and so on. Important: Deleted user settings cannot be restored after this action is taken.

When the software is run in safe mode, some functionality will not be available. The Workbench must be restarted normally to gain full functionality again.