Primer Design

Advanced and automated primer design tools support graphically and algorithmically advanced design of oligonucleotides – often referred to as oligos or primers.

A large number of criteria for the primer design can be user defined. Settings and adjustments of parameters results in dynamic updates of the primer calculations and the output of the calculations. The program thus offers full interactivity in your dynamic search for the best primers.

The Workbench also supports primer design of PCR primers and TaqMan probes based on an alignment of multiple sequences.

The primer design tools are part of both CLC Genomics Workbench and CLC Main Workbench.

Some of the advantages of the primer design tools are

  • State-of-the-art algorithms and parameters for predicting melting temperature
  • Advanced graphical overview of primers and probes, as well as their quality
  • Interactive design through dynamic updates of optimal primers at different parameters
  • Full integration with all other features of the Workbench
  • Support for a number of primer types: Standard PCR, Nested PCR, TaqMan PCR and Sequencing primers



Sequencing Data Analysis

DNA sequence reads from automated sequencing machines can be imported to the Workbench, trimmed and mapped to a reference sequence or assembled without use of reference sequence. A number of different file formats such as e.g. .SCF, .ABI, and PHD files are supported.

Interested in assembly of 454, Illumina Genome Analyzer, SOLiD or other high-throughput sequencing data? Get an overview of CLC Genomics Workbench

Sequencing reads can be assembled into contigs without use of reference sequence or they can be mapped to a reference. You can also assemble reads to an existing contig.
Residues that are different from the contig are colored, providing an overview of inconsistencies. A ‘Find Inconsistency’ option allows quick and easy inspection of called variations.

Traces, trimmed ends, coverage etc can be displayed for each contig and annotations, such as SNP annotations, can be added to regions of interest during the assembling process.

The Workbenches are also able to detect secondary peaks – a peak within a peak – to help discover heterozygous mutations. Looking at the height of the peak below the top peak, the Workbench considers all positions in a sequence, and if a peak is higher than the threshold set by the user, it will be “called”.

Due to the integrated nature of the CLC Workbench it is easy to use the created contig-sequence as input for additional analyses such as BLAST analysis or cloning construction.

Sequencing data analysis is easily done by using either CLC Main Workbench or CLC Genomics Workbench.

Some of the many advantages of our contig assembly framework are

  • Customized graphical display of trace data and quality scores
  • Automatic annotation of reference sequences with known SNP’s from the dbSNP database
  • An integrated framework allows the use of sequence annotation (such as SNP information) to guide the interpretation of assembly results
  • State-of-the-art assembly algorithms
  • Manual trimming or Automatic trimming of sequence reads based on quality scores, ambiguity characters and vector contamination
  • Trim cause no data to be deleted but adds an annotation to be considered by the assembly algorithm Quick-keys for fast manual inspection and editing of contigs
    Graphical illustration of read coverage for an easy overview of contig confidence



CLC Main Workbench and CLC Genomics Workbench offer graphically advanced in silico cloning, design of vectors for various purposes and tools to perform in silico Gateway cloning, including Multi-site Gateway cloning.

Our approach for visual cloning is based on another philosophy than most other software tools, as the users are in total in control of the cloning process – contrary to the more or less automatic and non-controllable cloning processes in other applications.

Advantages of our molecular cloning tools are

  • A graphically illustrated cloning process with total user control
  • Sequence detail functionality allows easy overview of all fragment ends and overhangs
    Highly flexible mouse-controlled DNA manipulation to accommodate all forms of restriction enzyme, exonuclease, and ligase activity
  • Advanced graphical display allows you to easily view and introduce cuts at restriction enzyme recognition sites
  • The option of introducing PCR fragments in the cloning process that are generated by the Primer Designer function, and have primer locations marked as annotation
  • All manipulations of sequences are done manually, giving you total control over how the sequence is constructed.


Expression Analysis

CLC Main Workbench and CLC Genomics Workbench are able to analyze expression data produced on microarray platforms. In addition, CLC Genomics Workbench can analyze next generation sequencing data.

The Workbenches provide tools for performing quality control of the data, transformation and normalization, statistical analysis to measure differential expression and annotation-based tests. A number of visualization tools such as volcano plots, MA plots, scatter plots, box plots and heat maps are used to aid the interpretation of the results.

Some of the features are

  • Support for both microarray- and sequencing-based (post-mapping RNA-Seq) expression data
  • Interactive heat map and scatter plots for visualization
  • Transformation and normalization tools
  • Quality control tools including principal component analysis, MA- and box plots
  • Experimental design tools for two- or multiple group comparisons
  • T-tests and ANOVA analysis with support for paired/repeated measures
  • Multiple testing corrected p-values (Bonferroni and/or FDR)
  • Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM)
  • Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. ‘GO’stats or specific protein pathways)


Multiple Sequence Alignment
All CLC bio’s workbenches include pairwise and multiple alignments of DNA, RNA, and protein sequences.

We have two proprietary alignment algorithms. An accurate alignment (recommended) and a fast alignment, particularly useful for datasets with very long sequences.
You can also run two other alignment methods by adding our Additional alignment plugin. This allows for use of ClustalW and Muscle.

For more detailed information on each of the alignment methods we encourage you to read the original research papers and the respective websites of the different methods. A recent paper describes some of the below mentioned algorithms and their strengths [Edgar and Batzoglou, 2006].

Multiple sequence alignment can be made with CLC Main Workbench or CLC Genomics Workbench.

Advanced alignment features include

  • A number of alignment editing options
  • Joining alignments – can be used to contruct “supergenes” for phylogenetic inference
  • Consensus sequence easily saved as a separate file for further analyses
  • Conservation of all sequence positions are shown below the alignment
  • Sequence logo displaying information content of all positions in the alignment
  • Copy annotations between sequences in alignments
  • Advanced pairwise comparison table for gaps, differences, distance and similarity



Workflows are easily built in our Workbench and combine various tools from the toolbox into one analysis.

A workflow consists of a series of tools where the output of one tool is connected as the input to another tool.

Once the workflow is set up, it can be installed (either in your own Workbench, on a Server, or sent to a colleague) and you can then analyze a lot of samples using the same standard pipeline with the same parameters.


3D viewer

It is fast and intuitive to customize the visualization of molecules. The molecules are automatically soreted in categories; proteins, nucleic acids, ligands, cofactors, and water molecules. A selection of visualization styles are readily accessible via quick-style buttons.

Proteins and nucleic acids can be visualized simultaneously in synchronized sequence and structure views, such that sequence annotation can be viewed in a 3D structural context.


CLC Main Workbench allows for creation and visualization of phylogenetic trees and associated metadata. It is easy e.g. to find the optimal statistical approach by model testing and visualize imported metadata on tree topology, at high quality, ready for publication.

There are options to easily modify tree layout and color scheme. Also tools for e.g. generating phylogenetic trees using K-mer based tree construction and for Maximum Likelihood analysis of amino acid alignments are available.

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