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Introduction to CLC Genomics Workbench
- Contact information
- System requirements
- Licenses
- About CLC Workbenches
- When the program is installed: Getting started
  - Quick start
  - Import of example data
- Plug-ins
- Network configuration
User interface
- View Area
- Zoom and selection in View Area
- Toolbox and Status Bar
- Workspace
- List of shortcuts
Data management and search
- Navigation Area
- Customized attributes on data locations
- Filling in values
  - What happens when the sequence gets outside the data location?
  - Searching
- Local search
User preferences and settings
- General preferences
- Default view preferences
  - Number formatting in tables
  - Import and export Side Panel settings
- Data preferences
- Advanced preferences
  - Default data location
  - NCBI BLAST
- Export/import of preferences
  - The different options for export and importing
- View settings for the Side Panel
  - Floating Side Panel
Printing
- Selecting which part of the view to print
- Page setup
  - Header and footer
- Print preview
Import/export of data and graphics
- Standard import
- Import high-throughput sequencing data
- Import tracks
- Data export
- Export graphics to files
- Export graph data points to a file
- Copy/paste view output
History log
- Element history
  - Sharing data with history
Batching and result handling
- Batch processing
- How to handle results of analyses
  - Table outputs
  - Batch log
Workflows
- Creating a workflow
- Distributing and installing workflows
- Executing a 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
- Creating a new sequence
- Sequence Lists
Data download
- GenBank search
- UniProt (Swiss-Prot/TrEMBL) search
- Search for structures at NCBI
- Download reference genome
  - Selecting data types for download
- Sequence web info
BLAST search
- Running BLAST searches
- Output from BLAST searches
- Local BLAST databases
- Manage BLAST databases
  - Migrating from a previous version of the Workbench
- Bioinformatics explained: BLAST
3D molecule viewing
- Importing structure files
- Viewing structure files
  - Moving and rotating
- Selections and display of the 3D structure
  - Coloring of the 3D structure
  - Hierarchical view - changing how selections of the structure are displayed
- 3D Output
General sequence analyses
- Shuffle sequence
- Dot plots
  - Create dot plots
  - View dot plots
- Bioinformatics explained: Dot plots
  - Realization of dot plots
  - Examples and interpretations of dot plots
- Bioinformatics explained: Scoring matrices
  - Different scoring matrices
  - Use of scoring matrices
- Local complexity plot
- Sequence statistics
  - Bioinformatics explained: Protein statistics
- Join sequences
- Pattern Discovery
  - Pattern discovery search parameters
  - Pattern search output
- Motif Search
Nucleotide analyses
- Convert DNA to RNA
- Convert RNA to DNA
- Reverse complements of sequences
- Reverse sequence
- Translation of DNA or RNA to protein
  - Translate part of a nucleotide sequence
- Find open reading frames
  - Open reading frame parameters
Protein analyses
- Signal peptide prediction
  - Signal peptide prediction parameter settings
  - Signal peptide prediction output
- Bioinformatics explained: Prediction of signal peptides
- Protein charge
  - Modifying the layout
- Transmembrane helix prediction
- Antigenicity
  - Plot of antigenicity
  - Antigenicity graphs along sequence
- Hydrophobicity
  - Hydrophobicity plot
  - Hydrophobicity graphs along sequence
- Bioinformatics explained: Protein hydrophobicity
  - Hydrophobicity scales
- Pfam domain search
  - Pfam search parameters
  - Download and installation of additional Pfam databases
- Secondary structure prediction
- Protein report
  - Protein report output
- Reverse translation from protein into DNA
  - Reverse translation parameters
- Bioinformatics explained: Reverse translation
- Proteolytic cleavage detection
  - Proteolytic cleavage parameters
- 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
  - User input
  - Standard PCR output table
- Nested PCR
  - Nested PCR output table
- TaqMan
  - TaqMan output table
- Sequencing primers
  - Sequencing primers output table
- 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
  - Scaling traces
  - Trace settings in the Side Panel
- Trim sequences
  - Manual trimming
  - Automatic trimming
- Assemble sequences
- Assemble to reference sequence
- Add sequences to an existing contig
- View and edit read mappings
- Reassemble contig
- Secondary peak calling
Cloning and cutting
- Molecular cloning
- Gateway cloning
- Restriction site analysis
- Dynamic restriction sites
- Restriction site analysis from the Toolbox
- Gel electrophoresis
- Restriction enzyme lists
  - Create enzyme list
  - View and modify enzyme list
Sequence alignment
- Create an alignment
- View alignments
- Bioinformatics explained: Sequence logo
  - Calculation of sequence logos
- Edit alignments
- Join alignments
  - How alignments are joined
- Pairwise comparison
- Bioinformatics explained: Multiple alignments
  - Use of multiple alignments
  - Constructing multiple alignments
Phylogenetic trees
- Inferring phylogenetic trees
  - Phylogenetic tree parameters
  - Tree View Preferences
- Bioinformatics explained: phylogenetics
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
- Trimming
- Multiplexing
  - Sort sequences by name
  - Process tagged sequences
- Sequencing data quality control
  - Report contents
  - Running the quality control tool
- 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
- Creating graph tracks
Read mapping
- The read mapper tool
- Mapping reports
  - Detailed mapping report
  - Summary mapping report
- Color space
- Mapping result
- Merge mapping results
- Extract consensus sequence
Resequencing
- Target regions statistics
- Quality-based variant detection
- Probabilistic variant detection
- Variant data
- Detailed information about overlapping paired reads
- Filtering and annotating variants
- Comparing variants
- Predicting functional consequences
Transcriptomics
- RNA-Seq analysis
- Expression profiling by tags
- Small RNA analysis
- Experimental design
- 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
Epigenomics
- ChIP sequencing
Appendix
- Comparison of workbenches
- Use of multi-core computers
- Graph preferences
- Working with tables
  - Filtering tables
- 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
- Microarray data formats
- Translation Tables
- Custom codon frequency tables
- 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