• 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

Other useful resources

The BLAST web page hosted at NCBI
http://www.ncbi.nlm.nih.gov/BLAST

Download pages for the BLAST programs
http://www.ncbi.nlm.nih.gov/BLAST/download.shtml

Download pages for pre-formatted BLAST databases
ftp://ftp.ncbi.nlm.nih.gov/blast/db/

O'Reilly book on BLAST
http://www.oreilly.com/catalog/blast/

Explanation of scoring/substitution matrices and more
http://www.clcbio.com/be/

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