Features and benefits of CLC Main Workbench

CLC Main Workbench includes all features and functions of CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench.

Assembly

CLC Main Workbench allows you to import, view, edit and analyze results from automated sequencing machines. Here, 3 sequencing reads have been automatically assem­bled into a contig sequence. The color intensity of each of the four nucleotides is shown as a trace graph under the called sequence of each sequencing read. The conflicts between the reads are marked with a red annotation.

Primer design
The primer design functionality in the workbench offers the user an unprecedented level of graphical interaction during the primer selection process. Primers can be de­signed for various experimental settings. In the primer ed­itor the user can easily select regions to define primer sets and immediately view the properties of all primers using various levels of detail. When primer selection criteria, such as melting temperature and self-annealing values are adjusted, the effect can be immediately evaluated. The integrated nature of the workbench makes it easy to design primers that span or cover a specific genetic ele­ment. Here the user has chosen to design primers that span a known genetic variation in an exon and requested that the primers must have a length between 18 and 22 nucleotides. Each available primer is indicated by a dot. Green dots indicate primers which fullfill all the selection criteria and red dots indicate primers which fail to meet one or more of the selection criteria.

RNA analysis
An optimal secondary structure has been predicted for a tRNA molecule. The figure below shows the predicted structure. The layout of the structure can be manually ed­ited by rotating the stems. Based on partition function, the coloring of the un-paired bases shows the probability that these bases will not be paired. Likewise, the probabilities of the paired bases can also be shown.

The CLC Workbench gives the user easy access to a range of complex al­gorithms and options for RNA analysis. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms and parameters, thermodynamic and statistical details are easily extracted and experimental information can be easily incorporated into the analysis. With the Workbench, RNA secondary structure information can be viewed and manipulated through a graphically and functionally advanced user inter­face. Through this, the user can simultaneously view linear, tabular, and 2D representations of RNA sequences and structures of choice.

Thermodynamic and statistical properties of secondary structure elements can be easily accessed. And secondary structures can be edited to facilitate interpretation and pub­lication.

Protein biochemistry
CLC Main Workbench has integrated viewing of three-dimensional structures in both PDB and mmCIF formats. Furthermore the 3D structures can be re­trieved directly from the Protein DataBank via integrated BLAST homology searches. Structures can be visualized in a range of ways, creating stunning graphics, which can be used for presentations and reports.

Alignment
Contrary to most other alignment programs, CLC Main Workbench allows you to show the annotations of the individual sequences in a multiple sequence alignment. This can easily identify whether certain domains are conserved throughout an alignment.

Moreover, the information content of the alignment can be shown in form of a sequence logo, which can show information on highly conserved regions. The conservation of the individual residues in the alignments is shown as a histogram below the alignment.

Cloning
CLC Main Workbench offers graphically advanced in silico cloning and design of vectors for various purposes. Our approach to 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. Adjustments of sequence overhangs by in silico nuclease treatment or filling in overhangs in both vector and insert are easily carried out and inspected visually.

BLAST/DB search
CLC Main Workbench offers to conduct BLAST searches on protein and DNA sequences or a combination of these using NCBI or it can run local if proprie­tary sequences are used. BLAST results are presented in a graphical overview together with a detailed tabular representation of the results. Sequence hits can easily be downloaded and analyzed further.

Moreover is it possible to annotate an input sequence with SNPs by BLASTing against the SNP database at NCBI. At the top is the alignment of all the hit sequences, and also displayed as annotations on the query sequence. At the bottom is a table showing all the hits which can be sorted and searched.

It is also possible to search your own data for homologous without the hassle of creating a BLAST database first. This can be done “on-the-fly” and can also be used to match primers against a larger sequence. Plug-ins

CLC bio’s modern and flexible IT architecture facilitates easy development of plug-ins for all of our bioinformatics workbenches, through our open API. When one or more plug-ins is installed on your computer, it is fully integrated with your CLC workbench – it runs as if it were one single (expanded) ap­plication.

You can develop your own plug-ins using our Developer Kit, or you can choose to use plug-ins developed by us or by third parties.

Import and export formats
CLC Main Workbench is extremely flexible in regard to importing and export­ing bioinformatics data. Sequences, alignments and phylogenetic trees can be imported and exported in a large number of formats: The advanced but easy-to-use graphics export allows you to use high-end graphic elements in presentations and papers on your research.

Simply adjust the layout of the element in the Workbench with graphs and colors, and press Graphics export. You can select from three bitmap formats: png, jpg and tiff, and four vector graphics formats: pdf, svg, ps and eps. When exporting bitmaps, the resolution can be adjusted to produce very high-qual­ity graphics.

Features and benefits of CLC Main Workbench

Features and benefits of CLC Main Workbench