Advanced and automated primer design tools support graphically and algorithmically advanced design of oligonucleotides – often referred to as oligos or primers.
Several criteria for primer design can be defined by the user. Adjusting settings and parameters results in dynamic updates of both the primer calculations and the output of the calculations. The program thus offers full interactivity in the dynamic search for the best primers.
The Workbench also supports design of PCR primers and TaqMan probes based on the 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
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 .SCF, .ABI, and PHD files are supported for Sanger sequencing reads.
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.
Nucleotides that are different from the contig are colored, providing an overview of inconsistencies. A ‘Find Inconsistency’ option allows quick and easy inspection of called variants.
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 in Sanger sequence chromatograms – 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
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.
You can easily import from other formats, e.g., VectorNTI sequences and databases, to have all your cloning experiments in one site.
Advantages of our molecular cloning tools are
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
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.
The Whole Genome Alignment tool, available as a plugin, makes it straight forward to undertake comparative sequence analysis of whole genomes and includes alignment of multiple genomes, calculating average nucleotide identities, visualizing genomic relationships and extracting multiple sequence alignments for further processing.
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
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.
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.