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Introduction to CLC Genomics Workbench
- Contact information and citation
- Download and installation
- System requirements
  - Limitations on maximum number of cores
- Workbench Licenses
- Plugins
- Network configuration
- CLC Server connection
- Getting started and 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
- 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
  - VCF import
- Import high-throughput sequencing data
- Import RNA spike-in controls
- Import Primers
  - Import Primer Pairs
- 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)
- SRA search
- Sequence web info
References management
- Download Genomes
- QIAGEN Sets
- Custom Sets
- Imported Data
  - Exporting reference data outside of the Reference Data Manager framework
Running tools, handling results and batching
- Running tools
- Handling results
  - Running a tool on a CLC Server
- 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
- Editing Metadata tables
Workflows
- Creating a workflow
- Editing existing workflows
  - Snippets in workflows
  - Workflow visualization
- Workflow elements
- Launching workflows individually and in batches
- Batching part of a workflow
- Advanced workflow batching
- Managing workflows
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
- 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
General sequence analyses
- 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
- 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
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
Tracks
- Track types
  - Visualizing, zooming and navigating tracks
  - Showing a track in a table
- Track lists
- Retrieving reference data tracks
- Merge Annotation Tracks
- Track Conversion
  - Convert to Tracks
  - Convert from Tracks
- Annotate and Filter
- Graphs
Prepare sequencing data
- QC for Sequencing Reads
- Trim Reads
- Demultiplex Reads
Quality control for resequencing analysis
- QC for Targeted Sequencing
- QC for Read Mapping
- Whole Genome Coverage Analysis
- Combine Reports
  - Report types supported
Read mapping
- Map Reads to Reference
- Reads tracks and stand-alone read mappings
- Local Realignment
- Merge Read Mappings
- Remove Duplicate Mapped Reads
  - Algorithm details and parameters
  - Running the duplicate reads removal
- Extract Consensus Sequence
Variant detection
- Variant Detection tools
- Fixed Ploidy Variant Detection
- Low Frequency Variant Detection
- Basic Variant Detection
- Variant Detection - filters
  - General filters
  - Noise filters
- Variant Detection - the outputs
- Fixed Ploidy and Low Frequency Detection tools: detailed descriptions
- Copy Number Variant Detection
- Identify Known Mutations from Sample Mappings
  - Run the Identify Known Mutations from Sample Mappings tool
  - Output from the Identify Known Mutations from Sample Mappings tool
- InDels and Structural Variants
Resequencing analysis
- Variant filtering
- Variant annotation
- Variants comparison
- Variant quality control
  - Create Variant Track Statistics Report
- Functional consequences
RNA-seq and Small RNA analysis
- RNA-seq normalization
- RNA-Seq Analysis
- PCA for RNA-Seq
  - Principal component analysis plot (2D)
  - Principal component analysis plot (3D)
- Differential Expression
- 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
  - Tool output and GAF file comparison
- miRNA analysis
Microarray 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
De Novo sequencing
- The CLC de novo assembly algorithm
- De Novo Assembly
- Map Reads to Contigs
Epigenomics analysis
- Histone Chip-Seq
- ChIP-Seq Analysis
- Annotate with nearby gene information
- Bisulfite Sequencing
- Advanced Peak Shape Tools
Utility tools
- Batch Rename
- Extract Annotations
- Sample reads
- Extract Reads
- Merge Overlapping Pairs
Legacy tools
- Compare Sample Variant Tracks
- Remove Reference Variants
- Reverse sequence
- Import Roche 454
- Create Combined RNA-Seq Report
- Create Track from Experiment
- Small RNA Analysis
- Batch launching workflows with multiple inputs
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
- 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

PAM60 log-odds matrix

	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
A	5	-5	-2	-1	-6	0	-5	-3	-5	-4	-3	-2	0	-3	-5	1	1	-1	-10	-6
C	-5	9	-10	-10	-9	-7	-6	-4	-10	-11	-10	-7	-6	-10	-6	-1	-5	-4	-12	-2
D	-2	-10	7	3	-11	-2	-2	-5	-2	-9	-7	2	-5	-1	-6	-2	-3	-6	-11	-8
E	-1	-10	3	7	-10	-2	-3	-4	-3	-7	-5	0	-3	2	-6	-2	-4	-4	-12	-7
F	-6	-9	-11	-10	8	-7	-4	-1	-10	-1	-2	-6	-7	-9	-7	-5	-6	-5	-3	3
G	0	-7	-2	-2	-7	6	-6	-7	-5	-8	-6	-1	-4	-5	-7	0	-3	-4	-11	-10
H	-5	-6	-2	-3	-4	-6	8	-6	-4	-4	-7	1	-2	2	0	-4	-5	-5	-5	-2
I	-3	-4	-5	-4	-1	-7	-6	7	-4	0	1	-4	-6	-5	-4	-4	-1	3	-10	-4
K	-5	-10	-2	-3	-10	-5	-4	-4	6	-6	0	0	-4	-1	2	-2	-2	-6	-8	-7
L	-4	-11	-9	-7	-1	-8	-4	0	-6	6	2	-5	-5	-3	-6	-6	-5	-1	-4	-5
M	-3	-10	-7	-5	-2	-6	-7	1	0	2	10	-6	-6	-2	-2	-4	-2	0	-9	-7
N	-2	-7	2	0	-6	-1	1	-4	0	-5	-6	6	-4	-2	-3	1	-1	-5	-6	-3
P	0	-6	-5	-3	-7	-4	-2	-6	-4	-5	-6	-4	7	-1	-2	0	-2	-4	-10	-10
Q	-3	-10	-1	2	-9	-5	2	-5	-1	-3	-2	-2	-1	7	0	-3	-4	-5	-9	-8
R	-5	-6	-6	-6	-7	-7	0	-4	2	-6	-2	-3	-2	0	8	-2	-4	-5	0	-8
S	1	-1	-2	-2	-5	0	-4	-4	-2	-6	-4	1	0	-3	-2	5	1	-4	-4	-5
T	1	-5	-3	-4	-6	-3	-5	-1	-2	-5	-2	-1	-2	-4	-4	1	6	-1	-9	-5
V	-1	-4	-6	-4	-5	-4	-5	3	-6	-1	0	-5	-4	-5	-5	-4	-1	6	-11	-5
W	-10	-12	-11	-12	-3	-11	-5	-10	-8	-4	-9	-6	-10	-9	0	-4	-9	-11	13	-3
Y	-6	-2	-8	-7	3	-10	-2	-4	-7	-5	-7	-3	-10	-8	-8	-5	-5	-5	-3	9