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Introduction to CLC Genomics Workbench
- Contact information
- Download and installation
- System requirements
  - Limitations on maximum number of cores
- Workbench Licenses
- When the program is installed: Getting started
  - Quick start
- Plugins
- Network configuration
- Latest improvements
User interface
- View Area
- Zoom and selection in View Area
- Toolbox and Status Bar
- Workspace
- List of shortcuts
Data management and search
- Navigation Area
- Metadata
- Working with tables
  - Filtering tables
- Customized attributes on data locations
- Local search
  - Quick search
  - Advanced search
User preferences and settings
- General preferences
- View preferences
  - Import and export Side Panel settings
- Data preferences
- Advanced preferences
- Export/import of preferences
- View settings for the Side Panel
Printing
- Selecting which part of the view to print
- Page setup
- Print preview
Import/export of data and graphics
- Standard import
  - External files
- Import tracks
  - GFF3 format
- Import high-throughput sequencing data
- Import RNA spike-in controls
- Data export
- Export graphics to files
  - File formats
- Export graph data points to a file
- Copy/paste view output
Data download
- Download reference genome data
  - Selecting data types for download
  - Cytogenetic ideograms
- Search for Sequences at NCBI
  - NCBI search options
  - Handling of NCBI search results
- Search for structures at NCBI
- UniProt (Swiss-Prot/TrEMBL) search
- SRA search
- Sequence web info
Running tools, handling results and batching
- Running tools
- Handling results
- Batch processing
Workflows
- Creating a workflow
- Distributing and installing workflows
- Executing a workflow
- Open copy of installed workflow
Viewing and editing sequences
- View sequence
- Circular DNA
  - Using split views to see details of the circular molecule
  - Mark molecule as circular and specify starting point
- Working with annotations
- Element information
- View as text
- Sequence Lists
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
3D Molecule Viewer
- Importing molecule structure files
- Viewing molecular structures in 3D
  - Updating old structure files
- Customizing the visualization
  - Visualization styles and colors
  - Project settings
- Tools for linking sequence and structure
- Protein structure alignment
General sequence analyses
- Extract Annotations
- 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
- Reverse sequence
- 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
- Pfam domain search
  - Download of Pfam database
  - Running Pfam Domain Search
- Secondary structure prediction
- Protein report
- Reverse translation from protein into DNA
  - Bioinformatics explained: Reverse translation
- Proteolytic cleavage detection
  - Bioinformatics explained: Proteolytic cleavage
Primers
- 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
Sequencing data analyses
- 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
Cutting and cloning
- Restriction site analyses
  - Dynamic restriction sites
  - Restriction Site Analysis
- Restriction enzyme lists
- Molecular cloning
- Gateway cloning
- Gel electrophoresis
  - Gel view
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
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
Trimming, multiplexing and sequencing quality control
- Trim Reads
- Demultiplex reads
  - An example using Illumina barcoded sequences
- Sequencing data quality control
- Merge overlapping pairs
  - Using quality scores when merging
  - Report of merged pairs
Tracks
- Track lists
- Retrieving reference data tracks
- Merging tracks
- Converting data to tracks and back
  - Convert to tracks
  - Convert from tracks
- Annotate and filter tracks
- Graphs
Read mapping
- Map Reads to Reference
- Mapping output
- Mapping reports
  - Summary mapping report
  - Detailed mapping report
- Mapping SOLid reads in color space
  - Viewing color space information
  - Mapping in color space
- Local realignment
- Merge mapping results
- Remove duplicate mapped reads
  - Algorithm details and parameters
  - Running the duplicate reads removal
- Extract consensus sequence
- Sample reads
Resequencing
- Create Statistics for Target Regions
- InDels and Structural Variants
- Coverage analysis
- Variant Detectors - overview
  - Differences in the variants called by the different tools
  - How the variant detection tools work
- Fixed Ploidy Variant Detection
  - Ploidy and sensitivity
- Low Frequency Variant Detection
- Basic Variant Detection
- Variant Detectors - error model estimation
- Variant Detectors - filters
  - General filters
  - Noise filters
- Variant Detectors - the outputs
- The Fixed Ploidy and Low Frequency variant callers: detailed descriptions
  - The Fixed Ploidy Variant Caller: Models and methods
  - The Low Frequency Variant caller: Models and methods
- Variant data
- Detailed information about overlapping paired reads
- Annotate and filter variants
- Comparing variants
- Predicting functional consequences
- Identify Known Mutations from Sample Mappings
  - How to run the Identify Known Mutations from Sample Mappings tool
  - Output from the Identify Known Mutations from Sample Mappings tool
RNA-Seq Analysis tools
- RNA-Seq analysis
- Create Combined RNA-Seq Report
- Advanced RNA-Seq Tools
  - TMM Normalization
  - Metadata for RNA-Seq
- PCA for RNA-Seq
  - Principal component analysis plot (2D)
  - Principal component analysis plot (3D)
- Differential Expression for RNA-Seq
- Create Heat Map for RNA-Seq
  - Clustering of features and samples
  - The heat map view
- Create Expression Browser
  - The expression browser
- Create Venn Diagram for RNA-Seq
  - Venn diagram table view
- Gene Set Test
Microarray and Small RNA Analysis
- Small RNA analysis
- Experimental design
- Working with tracks and experiments
- Transformation and normalization
- Quality control
- Statistical analysis - identifying differential expression
- Feature clustering
  - Hierarchical clustering of features
  - K-means/medoids clustering
- Annotation tests
  - Hypergeometric tests on annotations
  - Gene set enrichment analysis
- General plots
De novo sequencing
- De novo assembly
- Map Reads to Contigs
Epigenomics
- ChIP-Seq Analysis
- Annotate with nearby gene information
Legacy tools
- Import Roche 454
- Import SOLiD
Appendix
- Use of multi-core computers
- 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
- SAM/BAM export format specification
  - Flags
- Gene expression annotation files and microarray data formats
- Translation Tables
- Custom codon frequency tables
- Comparison of track comparison tools
- Matrices for alignment calculation
Bibliography

Structure elements and their energy contribution

In this section, we classify the structure elements defining a secondary structure and describe their energy contribution.

Image RNA_structure_prediction_web
Figure 21.29: The different structure elements of RNA secondary structures predicted with the free energy minimization algorithm in CLC Genomics Workbench. See text for a detailed description.

Subsections