• Manuals

Browse the manual

• Introduction to CLC Genomics Workbench
  • Contact information
  • System requirements
  • Licenses
    • Request an evaluation license
    • Download a license
    • Import a license from a file
    • Upgrade license
    • Configure license server connection
    • Limited mode
  • About CLC Workbenches
    • New program feature request
    • Getting help
    • CLC Sequence Viewer vs. Workbenches
  • When the program is installed: Getting started
    • Quick start
    • Import of example data
  • Plug-ins
    • Installing plug-ins
    • Uninstalling plug-ins
    • Updating plug-ins
    • Resources
  • Network configuration
• User interface
  • View Area
    • Open view
    • Show element in another view
    • Close views
    • Save changes in a view
    • Undo/Redo
    • Arrange views in View Area
    • Side Panel
  • Zoom and selection in View Area
    • Zoom In
    • Zoom Out
    • Fit Width
    • Zoom to 100%
    • Move
    • Selection
    • Changing compactness
  • Toolbox and Status Bar
    • Processes
    • Toolbox
    • Status Bar
  • Workspace
    • Create Workspace
    • Select Workspace
    • Delete Workspace
  • List of shortcuts
• Data management and search
  • Navigation Area
    • Data structure
    • Create new folders
    • Sorting folders
    • Multiselecting elements
    • Moving and copying elements
    • Change element names
    • Delete elements
    • Show folder elements in a table
  • Customized attributes on data locations
    • Configuring which fields should be available
    • Editing lists
    • Removing attributes
    • Changing the order of the attributes
  • Filling in values
    • What happens when the sequence gets outside the data location?
    • Searching
  • Local search
    • What kind of information can be searched?
    • Quick search
    • Advanced search
    • Search index
• 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 using the import dialog
    • Import using drag and drop
    • Import using copy/paste of text
    • External files
  • Import high-throughput sequencing data
    • 454 from Roche Applied Science
    • Illumina
    • SOLiD from Life Technologies
    • Fasta format
    • Sanger sequencing data
    • Ion Torrent PGM from Life Technologies
    • Complete Genomics
    • General notes on handling paired data
    • SAM and BAM mapping files
  • Import tracks
  • Data export
  • Export graphics to files
    • Which part of the view to export
    • Save location and file formats
    • Graphics export parameters
    • Exporting protein reports
  • 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
    • Batch overview
    • Batch filtering and counting
    • Setting parameters for batch runs
    • Running the analysis and organizing the results
    • Running de novo assembly and read mapping in batch
  • How to handle results of analyses
    • Table outputs
    • Batch log
• Workflows
  • Creating a workflow
    • Adding workflow elements
    • Configuring workflow elements
    • Locking and unlocking parameters
    • Connecting workflow elements
    • Input and output
    • Workflow validation
    • Workflow creation helper tools
    • Supported data flows
  • Distributing and installing workflows
    • Creating a workflow installation file
    • Installing a workflow
    • Workflow identification and versioning
  • Executing a workflow
• Viewing and editing sequences
  • View sequence
    • Sequence settings in Side Panel
    • Restriction sites in the Side Panel
    • Selecting parts of the sequence
    • Editing the sequence
    • Sequence region types
  • Circular DNA
    • Using split views to see details of the circular molecule
    • Mark molecule as circular and specify starting point
  • Working with annotations
    • Viewing annotations
    • Adding annotations
    • Edit annotations
    • Removing annotations
  • Element information
  • View as text
  • Creating a new sequence
  • Sequence Lists
    • Graphical view of sequence lists
    • Sequence list table
    • Extract sequences
• Data download
  • GenBank search
    • GenBank search options
    • Handling of GenBank search results
    • Save GenBank search parameters
  • UniProt (Swiss-Prot/TrEMBL) search
    • UniProt search options
    • Handling of UniProt search results
    • Save UniProt search parameters
  • Search for structures at NCBI
    • Structure search options
    • Handling of NCBI structure search results
    • Save structure search parameters
  • Download reference genome
    • Selecting data types for download
  • Sequence web info
    • Google sequence
    • NCBI
    • PubMed References
    • UniProt
    • Additional annotation information
• BLAST search
  • Running BLAST searches
    • BLAST at NCBI
    • BLAST a partial sequence against NCBI
    • BLAST against local data
    • BLAST a partial sequence against a local database
  • Output from BLAST searches
    • Graphical overview for each query sequence
    • Overview BLAST table
    • BLAST graphics
    • BLAST table
    • Extracting a consensus sequence from a BLAST result
  • Local BLAST databases
    • Make pre-formatted BLAST databases available
    • Download NCBI pre-formatted BLAST databases
    • Create local BLAST databases
  • Manage BLAST databases
    • Migrating from a previous version of the Workbench
  • Bioinformatics explained: BLAST
    • Examples of BLAST usage
    • Searching for homology
    • How does BLAST work?
    • Which BLAST program should I use?
    • Which BLAST options should I change?
    • Explanation of the BLAST output
    • I want to BLAST against my own sequence database, is this possible?
    • What you cannot get out of BLAST
    • Other useful resources
• 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
    • Dynamic motifs
    • Motif search from the Toolbox
    • Java regular expressions
    • 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
    • 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
    • Why the interest in signal peptides?
    • Different types of signal peptides
    • Prediction of signal peptides and subcellular localization
    • The SignalP method
    • What do the SignalP scores mean?
  • 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
    • The Genetic Code
    • Challenge of reverse translation
    • Solving the ambiguities of 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
    • Saving primers
    • Saving PCR fragments
    • Adding primer binding annotation
  • 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
    • Specific options for alignment-based primer and probe design
    • Alignment based design of PCR primers
    • Alignment-based TaqMan 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
    • View settings in the Side Panel
    • Editing the read mapping
    • Sorting reads
    • Read conflicts
    • Output from the mapping
    • Extract parts of a mapping
    • Variance table
  • Reassemble contig
  • Secondary peak calling
• Cloning and cutting
  • Molecular cloning
    • Introduction to the cloning editor
    • The cloning work flow
    • Manual cloning
    • Insert restriction site
  • Gateway cloning
    • Add attB sites
    • Create entry clones (BP)
    • Create expression clones (LR)
  • Restriction site analysis
  • Dynamic restriction sites
    • Sort enzymes
    • Manage enzymes
    • Show enzymes cutting inside/outside selection
    • Show enzymes with compatible ends
  • Restriction site analysis from the Toolbox
    • Selecting, sorting and filtering enzymes
    • Number of cut sites
    • Output of restriction map analysis
    • Restriction sites as annotation on the sequence
    • Table of restriction sites
    • Table of restriction fragments
    • Gel
  • Gel electrophoresis
    • Separate fragments of sequences on gel
    • Separate sequences on gel
    • Gel view
  • Restriction enzyme lists
    • Create enzyme list
    • View and modify enzyme list
• Sequence alignment
  • Create an alignment
    • Gap costs
    • Fast or accurate alignment algorithm
    • Aligning alignments
    • Fixpoints
  • View alignments
  • Bioinformatics explained: Sequence logo
    • Calculation of sequence logos
  • Edit alignments
    • Move residues and gaps
    • Insert gaps
    • Delete residues and gaps
    • Copy annotations to other sequences
    • Move sequences up and down
    • Delete, rename and add sequences
    • Realign selection
  • Join alignments
    • How alignments are joined
  • Pairwise comparison
    • Pairwise comparison on alignment selection
    • Pairwise comparison parameters
    • The pairwise comparison table
  • 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
    • The phylogenetic tree
    • Modern usage of phylogenies
    • Reconstructing phylogenies from molecular data
    • Interpreting phylogenies
• RNA structure
  • RNA secondary structure prediction
    • Selecting sequences for prediction
    • Structure output
    • Partition function
    • Advanced options
    • Structure as annotation
  • View and edit secondary structures
    • Graphical view and editing of secondary structure
    • Tabular view of structures and energy contributions
    • Symbolic representation in sequence view
    • Probability-based coloring
  • 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
    • Quality trimming
    • Adapter trimming
    • Length trimming
    • Trim output
  • 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
    • Zooming and navigating track views
    • Adding, removing and reordering tracks
    • Showing a track in a table
    • Finding annotations on the genome
  • Retrieving reference data tracks
  • Merging tracks
  • Converting data to tracks and back
    • Convert to tracks
    • Convert from tracks
  • Annotate and filter tracks
    • Annotate from overlapping annotations
    • Filter annotations on name
    • Filter against overlapping annotations
  • Creating graph tracks
• Read mapping
  • The read mapper tool
    • Selecting reads and reference
    • Including or excluding regions (masking)
    • Mapping parameters
    • Mapping output
  • Mapping reports
    • Detailed mapping report
    • Summary mapping report
  • Color space
    • Sequencing
    • Error modes
    • Mapping in color space
    • Viewing color space information
  • Mapping result
    • Mapping table
    • View settings in the Side Panel
    • Output from the mapping
    • Extract parts of a mapping
    • Find broken pair mates
  • Merge mapping results
  • Extract consensus sequence
• Resequencing
  • Target regions statistics
    • Running the target regions statistics
    • Coverage summary report
    • Per-region statistics
    • Coverage table
  • Quality-based variant detection
    • Assessing the quality of the neighborhood bases
    • Significance of variant
    • Ploidy and genetic code
    • Reporting the variants
  • Probabilistic variant detection
    • Calculation of the prior and error probabilities
    • Calculation of the likelihood
    • Calculation of the posterior probability for each site type at each position in the genome
    • Comparison with the reference sequence and identification of candidate variants
    • Posterior filtering and reporting of variants
    • Running the variant detection
    • Setting ploidy and genetic code
    • Reporting the variants found
  • Variant data
    • Variant tracks
    • Annotated variant table
    • Linking adjacent variants in linkage groups
    • Variant types
    • Special notes upgrading to Genomics Workbench 6.0
  • Detailed information about overlapping paired reads
  • Filtering and annotating variants
    • Filter against known variants
    • Annotating from known variants
    • Exon number annotation
    • Annotate with flanking sequence
    • Filter marginal variants
    • Filter reference variants
  • Comparing variants
    • Compare variants within group
    • Fisher exact test
    • Trio analysis
    • Filter against control reads
  • Predicting functional consequences
    • Amino acid changes
    • Splice site effect prediction
    • GO enrichment analysis
    • Conservation score annotation
• Transcriptomics
  • RNA-Seq analysis
    • Defining reference genome and mapping settings
    • Exon identification and discovery
    • RNA-Seq output options
    • Interpreting the RNA-Seq analysis result
  • Expression profiling by tags
    • Extract and count tags
    • Create virtual tag list
    • Annotate tag experiment
  • Small RNA analysis
    • Extract and count
    • Downloading miRBase
    • Annotating and merging small RNA samples
    • Working with the small RNA sample
    • Exploring novel miRNAs
  • Experimental design
    • Supported array platforms
    • Setting up an experiment
    • Organization of the experiment table
    • Adding annotations to an experiment
    • Scatter plot view of an experiment
    • Cross-view selections
  • Transformation and normalization
    • Selecting transformed and normalized values for analysis
    • Transformation
    • Normalization
  • Quality control
    • Creating box plots - analyzing distributions
    • Hierarchical clustering of samples
    • Principal component analysis
  • Statistical analysis - identifying differential expression
    • Gaussian-based tests
    • Tests on proportions
    • Corrected p-values
    • Volcano plots - inspecting the result of the statistical analysis
  • Feature clustering
    • Hierarchical clustering of features
    • K-means/medoids clustering
  • Annotation tests
    • Hypergeometric tests on annotations
    • Gene set enrichment analysis
  • General plots
    • Histogram
    • MA plot
    • Scatter plot
• De novo sequencing
  • De novo assembly
    • How it works
    • Resolve repeats using reads
    • Automatic paired distance estimation
    • Optimization of the graph using paired reads
    • Bubble resolution
    • Converting the graph to contig sequences
    • Summary
    • Randomness in the results
    • SOLiD data support in de novo assembly
    • De novo assembly parameters
    • De novo assembly report
• Epigenomics
  • ChIP sequencing
    • Peak finding and false discovery rates
    • Peak refinement
    • Reporting the results
• Appendix
  • Comparison of workbenches
  • Use of multi-core computers
  • Graph preferences
  • Working with tables
    • Filtering tables
  • BLAST databases
    • Peptide sequence databases
    • Nucleotide sequence databases
    • Adding more 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
    • SAM Specification
    • SAM Header Section
    • SAM Alignment Section
    • Flags
    • Optional fields in the alignment section
  • Microarray data formats
    • GEO (Gene Expression Omnibus)
    • Affymetrix GeneChip
    • Illumina BeadChip
    • Gene ontology annotation files
    • Generic expression and annotation data file formats
  • Translation Tables
    • 1. Standard
    • 2. Vertebrate Mitochondrial
    • 3. Yeast Mitochondrial
    • 4. Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
    • 5. Invertebrate Mitochondrial
    • 6. Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear
    • 9. Echinoderm Mitochondrial; Flatworm Mitochondrial
    • 10. Euplotid Nuclear
    • 11. Bacterial and Plant Plastid
    • 12. Alternative Yeast Nuclear
    • 13. Ascidian Mitochondrial
    • 14. Alternative Flatworm Mitochondrial
    • 15. Blepharisma Macronuclear
    • 16. Chlorophycean Mitochondrial
    • 17. Trematode Mitochondrial
    • 18. Scenedesmus obliquus mitochondrial
    • 19. Thraustochytrium mitochondrial code
  • Custom codon frequency tables
  • Matrices for alignment calculation
    • PAM30 log-odds matrix
    • PAM60 log-odds matrix
    • BLOSUM42 log-odds matrix
    • BLOSUM62 log-odds matrix
    • BLOSUM80 log-odds matrix
• Bibliography

Comparison of workbenches

Below we list a number of functionalities that differ between CLC Workbenches and the CLC Sequence Viewer:

• CLC Sequence Viewer ()
• CLC Main Workbench ()
• CLC Genomics Workbench ()

	Data handling	Viewer	Main	Genomics
	Add multiple locations to Navigation Area
	Share data on network drive
	Search all your data

	Assembly of sequencing data	Viewer	Main	Genomics
	Advanced contig assembly
	Importing and viewing trace data
	Trim sequences
	Assemble without use of reference sequence
	Map to reference sequence
	Assemble to existing contig
	Viewing and edit contigs
	Tabular view of an assembled contig (easy data overview)
	Secondary peak calling
	Multiplexing based on barcode or name

	Next-generation Sequencing Data Analysis	Viewer	Main	Genomics
	Import of 454, Illumina Genome Analyzer, SOLiD and Helicos data
	Reference assembly of human-size genomes
	De novo assembly
	SNP/DIP detection
	Graphical display of large contigs
	Support for mixed-data assembly
	Paired data support
	RNA-Seq analysis
	Expression profiling by tags
	ChIP-Seq analysis

	Expression Analysis	Viewer	Main	Genomics
	Import of Illumina BeadChip, Affymetrix, GEO data
	Import of Gene Ontology annotation files
	Import of Custom expression data table and Custom annotation files
	Multigroup comparisons
	Advanced plots: scatter plot, volcano plot, box plot and MA plot
	Hierarchical clustering
	Statistical analysis on count-based and gaussian data
	Annotation tests
	Principal component analysis (PCA)
	Hierarchical clustering and heat maps
	Analysis of RNA-Seq/Tag profiling samples

	Molecular cloning	Viewer	Main	Genomics
	Advanced molecular cloning
	Graphical display of in silico cloning
	Advanced sequence manipulation

	Database searches	Viewer	Main	Genomics
	GenBank Entrez searches
	UniProt searches (Swiss-Prot/TrEMBL)
	Web-based sequence search using BLAST
	BLAST on local database
	Creation of local BLAST database
	PubMed lookup
	Web-based lookup of sequence data
	Search for structures (at NCBI)

	General sequence analyses	Viewer	Main	Genomics
	Linear sequence view
	Circular sequence view
	Text based sequence view
	Editing sequences
	Adding and editing sequence annotations
	Advanced annotation table
	Join multiple sequences into one
	Sequence statistics
	Shuffle sequence
	Local complexity region analyses
	Advanced protein statistics
	Comprehensive protein characteristics report

	Nucleotide analyses	Viewer	Main	Genomics
	Basic gene finding
	Reverse complement without loss of annotation
	Restriction site analysis
	Advanced interactive restriction site analysis
	Translation of sequences from DNA to proteins
	Interactive translations of sequences and alignments
	G/C content analyses and graphs

	Protein analyses	Viewer	Main	Genomics
	3D molecule view
	Hydrophobicity analyses
	Antigenicity analysis
	Protein charge analysis
	Reverse translation from protein to DNA
	Proteolytic cleavage detection
	Prediction of signal peptides (SignalP)
	Transmembrane helix prediction (TMHMM)
	Secondary protein structure prediction
	PFAM domain search

	Sequence alignment	Viewer	Main	Genomics
	Multiple sequence alignments (Two algorithms)
	Advanced re-alignment and fix-point alignment options
	Advanced alignment editing options
	Join multiple alignments into one
	Consensus sequence determination and management
	Conservation score along sequences
	Sequence logo graphs along alignments
	Gap fraction graphs
	Copy annotations between sequences in alignments
	Pairwise comparison

	RNA secondary structure	Viewer	Main	Genomics
	Advanced prediction of RNA secondary structure
	Integrated use of base pairing constraints
	Graphical view and editing of secondary structure
	Info about energy contributions of structure elements
	Prediction of multiple sub-optimal structures
	Evaluate structure hypothesis
	Structure scanning
	Partition function

	Dot plots	Viewer	Main	Genomics
	Dot plot based analyses

	Phylogenetic trees	Viewer	Main	Genomics
	Neighbor-joining and UPGMA phylogenies
	Maximum likelihood phylogeny of nucleotides

	Pattern discovery	Viewer	Main	Genomics
	Search for sequence match
	Motif search for basic patterns
	Motif search with regular expressions
	Motif search with ProSite patterns
	Pattern discovery

	Primer design	Viewer	Main	Genomics
	Advanced primer design tools
	Detailed primer and probe parameters
	Graphical display of primers
	Generation of primer design output
	Support for Standard PCR
	Support for Nested PCR
	Support for TaqMan PCR
	Support for Sequencing primers
	Alignment based primer design
	Alignment based TaqMan probe design
	Match primer with sequence
	Ordering of primers
	Advanced analysis of primer properties

	Molecular cloning	Viewer	Main	Genomics
	Advanced molecular cloning
	Graphical display of in silico cloning
	Advanced sequence manipulation

	Virtual gel view	Viewer	Main	Genomics
	Fully integrated virtual 1D DNA gel simulator

For a more detailed comparison, we refer to http://www.clcbio.com/compare.

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