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Introduction to CLC Main Workbench
- Contact information and citation
- Download and installation
- System requirements
  - Limitations on maximum number of cores
- Workbench Licenses
- Plugins
- Network configuration
- History of the CLC Workbenches
User interface
- View Area
- Zoom functionality in the View Area
- Toolbox and Favorites tabs
  - Toolbox tab
  - Favorites tab
- Processes tab and Status bar
- History and Element Info views
- Workspace
- List of shortcuts
Data management and search
- Navigation Area
- Working with tables
  - Filtering tables
- Customized attributes on data locations
- Searching for data in CLC Locations
  - Quick Search
  - Local Search
User preferences and settings
- General preferences
- View preferences
  - Import and export Side Panel settings
- 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
- AWS Connections
Import/export of data and graphics
- Standard import
  - External files
- Data export
- Export graphics to files
  - File formats
- Export graph data points to a file
- CLC Server data import and export
- Copy/paste view output
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
- Managing workflows
Viewing and editing sequences
- Sequence Lists
- View sequences
- Working with annotations
- 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
- K-mer Based Tree Construction
- Create tree
- Model Testing
- Maximum Likelihood Phylogeny
  - Bioinformatics explained
- Tree Settings
- Metadata and phylogenetic trees
General sequence analyses
- Annotate with GFF/GTF/GVF file
- Extract sequences
- Shuffle sequence
- Dot plots
- Local complexity plot
- Sequence statistics
  - Bioinformatics explained: Protein statistics
- Join Sequences
- Pattern discovery
  - Pattern discovery search parameters
  - Pattern search output
- Motif Search
- Create motif list
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
  - Open reading frame parameters
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 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
- Combine Reports
  - Combine Reports output
Primers and probes
- Primer design - an introduction
  - General concept
  - Scoring primers
- Setting parameters for primers and probes
  - Primer Parameters
- 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
  - Binding parameters
  - Results - binding sites and fragments
- Order primers
Cloning and restriction sites
- Restriction site analyses
- Restriction enzyme lists
- Restriction Based Cloning
- Homology Based Cloning
- Gateway 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
- Running BLAST searches
  - BLAST at NCBI
  - BLAST against local data
- Output from BLAST searches
- Local BLAST databases
- Manage BLAST databases
- Bioinformatics explained: BLAST
Utility tools
- Extract Annotated Regions
- Create Sequence List
- Update Sequence Attributes in Lists
- Split Sequence List
- Rename Elements
- Rename Sequences in Lists
Appendix
- Graph preferences
- BLAST databases
- 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
- Translation Tables
- Custom codon frequency tables
- Matrices for alignment calculation
Bibliography

Where can I get the BLAST+ programs

The BLAST+ package can be downloaded for use on your own computer, institution computer cluster or similar from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/. It is available for a wide range of different operating systems.

Pre-formatted databases are available from a dedicated BLAST ftp site ftp://ftp.ncbi.nlm.nih.gov/blast/db/. Most BLAST databases on the NCBI site are updated on a daily basis.

A few commercial software packages are available for searching your own data. The advantage of using a commercial program is obvious when BLAST is integrated with the existing tools of these programs. Furthermore, they let you perform BLAST searches and retain annotations on the query sequence (see figure 24.21). It is also much easier to batch download a selection of hit sequences for further inspection.

Image workbenchblastalignments_web
Figure 24.21: Snippet of alignment view of BLAST results. Individual alignments are represented directly in a graphical view. The top sequence is the query sequence and is shown with a selection of annotations.