You can’t even begin to understand biology, you can’t understand life, unless you understand what it’s all there for, how it arose – and that means evolution. – Richard Dawkins
Biology is not merely a mixture of macromolecular chemicals – DNA, RNA, or protein but the dynamic force for life and existence. Therefore the analysis and research of these chemicals to the core is important.
Today we will discuss about a powerful Bioinformatical tool. In this QIAGEN CLC Main Workbench review article, I bring you the ups and downs of the program. This write-up shall cover all the major areas of the CLC Main Workbench like features, pricing, pros, cons, limitations, etc.
Hope this review helps you in identifying your ideal Bioinformatical research tool!
What Is CLC Main Workbench?
CLC Main Workbench is a platform that is used by thousands of scientific researchers across the world for DNA, RNA, and protein sequence data analysis. It allows several data manipulations and executions of algorithms.
The intuitive user interface makes it a comfortable work environment for the user. No advanced computational skills are required to use CLC Main Workbench.
CLC Main Workbench is a complete and all-rounder package for thorough analysis. The various tools and features of CLC Main Workbench are mentioned below:
 Sequence Editing and Viewing
This feature offers to view the sequence. On double-clicking the sequence in the navigation area, the sequence of amino acid or DNA or RNA will appear on the view panel.
- You can zoom in, zoom out, and edit the sequence. There are several choices in Sequence Layout.
- Spacing- no spacing, every 10 residues, every 3 residues frame 1, every 3 residues frame 2, every 3 residues frame 3.
- Wrap sequences- no wrap, automatic wrap, fixed wrap
- Double-stranded- applies only to the double-stranded DNA sequence
- The position of sequences- shows the position of residue in a protein/DNA sequence.
- Sequence label- adding details such as name, accession, common name, etc. to the sequence.
- Annotation type and layouts, restriction sites, motifs, the coloring of residues
- DNA and Protein basic information
- Find function to search within a sequence
- Editing texts, sequences
- Studying and analyzing circular DNA
 3D Molecule Viewer
This feature is excellent. It allows the importing of molecule structure files from the Protein Data Bank (PDB) or its file in the system.
- You can view the protein structure in 3D. The visualization can be customized with different colors and styles of representation. The visualization settings include- hydrogens, fog, clipping plane, 3D projection, coloring, etc.
- You can BLAST search the structure file against the PDB database.
- There are some tools present in the 3D viewer that helps in linking the sequence and the structure. They link the sequence alignments to the molecule structure. The transfer of annotation between the sequence and structure is feasible too.
- The Protein structures can be aligned too.
- The “Generate Biomolecule” option lets you generate biomolecules structures in CLC Main Workbench. A file with information on 3D Coordinates only can be used to generate entire structures. Given below is a biomolecule structure generated from PDB 2R9R.
 Sequence Alignment
CLC Main Workbench is efficient in aligning the nucleotides and proteins by using the Progressive alignment algorithms. This alignment algorithm has three parameters for calculating the gap costs.
- CLC Main Workbench utilizes two algorithms for finding the alignments. One of them is fast and less accurate, while the other is slow and very accurate.
- Alignments can be viewed via Alignment info and Nucleotide info options.
- Just like any other sequence alignment tool, it displays the aligned regions and gaps. The extra choice of editing the alignments is provided here. You can add gaps, delete gaps, copy annotations to other sequences, etc.
- The realignment option lets you create alignment again. It is a powerful tool for editing alignments. It lets you remove changes, adjust the gaps, and edit the fixpoints.
- Join the alignments after you have edited them.
- You can even perform the pairwise comparisons, create comparison tables too.
- Multiple sequences can be aligned too to identify the mutations caused over time. A great way to realize the evolutionary change that might have occurred.
 Evolutionary Relationships
This is a key aspect in understanding the ancient genetic relations between different groups of organisms. The phylogenetic tree construction makes the understanding of such relations easier.
- CLC Main Workbench phylogenetic tree editor allows you to have- circular and radial layouts, data import in CSV format, a tabular representation of metadata, collapsing nodes based on bootstrap values, re-arranging the nodes, visualization of metadata, coloring, and labeling of trees, curved edges, editable nodes, and line size, etc.
- You can construct the tree by these two methods- UPGMA and Neighbourhood Joining method. After construction, you can check the reliability of the result by Bootstrapping.
- Another method of tree construction is the Maximum Likelihood phylogenetic tree.
- You can always adjust the tree layout settings. It can be saved for every tree construction you perform in the future.
- A minimap is an interesting tool that helps in viewing the tree in a very small area.
 General Bioinformatical Analysis
This list of tools lets you analyze the sequences and molecules in a broadway. You can extract the sequences, shuffle them, align them, and view them.
- You can construct the dot plots. They are a powerful visual representation for comparing two sequences.
- You can also calculate the local complexity for both DNA and protein sequences. It is a measure of the diversity in amino acid composition in a protein sequence. Uses the K2 algorithm.
- The general sequence statistics can also be calculated. CLC Main Workbench allows you to find the relevant numbers and figures for any two sequences or more. There are two methods- individual statistics layout and comparative statistics layout.
- For protein sequences, molecular weight, isoelectric points, and aliphatic index can be calculated. You can also estimate the half-life and extinction coefficient.
- CLC Main Workbench allows you to join several sequences together after editing. This leads to the development of “supergenes” that helps in phylogenetic inferences.
 Nucleotide Manipulations/ Analysis
The DNA can be converted to RNA and vice versa. You can reverse complement the sequences. The translation of DNA or RNA to proteins can be done virtually.
CLC Main Workbench allows us to find the open reading frames in a sequence.
 Protein Analysis
CLC Main Workbench lets you analyze a stretch of amino acid anyway you want to. You can estimate the protein charge, antigenicity, hydrophobicity through graphs.
- You can download it from the Pfam database. You can also perform a Pfam domain search.
- You can visualize the 3D protein structure from the database. Perform the model structure search to create models and predict models.
- The secondary structure of a protein can be predicted
- Protein reports can be obtained
- Reverse translation – protein to DNA conversion
- Proteolytic cleavage can be detected
 Cloning and Restriction Sites Identification
Restriction sites can be identified and analyzed. Restriction sites can be created and analyzed. The entire restriction enzyme list can be created.
- CLC Main Workbench lets you create molecular clones and allows editing too. You can insert the restriction sites at the preferred locations. It is manual cloning, hence user experience is quite commendable here.
- Gateway cloning is another added advantage of this feature. You can create entry clones and expression clones.
- A virtual Gel Electrophoresis can be performed and analyzed.
 RNA Structure Prediction
CLC Main Workbench lets you predict the secondary structure of RNA. You can view and edit the secondary structure of RNA. Graphical view and tabular view are feasible. The energy distributions can be studied.
- You can evaluate the structure hypothesis. You can select the sequences for evaluation.
- Construct the structure scanning plot.
The QIAGEN CLC Main Workbench has been cited in several research papers. Some of them include:
- Chicken Interferome: Avian Interferon-Stimulated Genes Identified by Microarray and RNA-seq of Primary Chick Embryo Fibroblasts Treated with a Chicken Type I Interferon (IFN-α)
- Genome-based Microbial Ecology of Anammox Granules in a Full-scale Wastewater Treatment System
- Transcriptomic Analysis of Staphylococcus epidermidis Biofilm-Released Cells upon Interaction with Human Blood Circulating Immune Cells and Soluble Factor: This paper was based on the sequence editing, trimming, alignment, read normalization, and expression analysis of the biofilm-forming bacteria.
For finding the actual commercial prices of the CLC Main Workbench you have to visit the official website and Request a quote.
You can also register yourself on their website and download the software CLC Main Workbench.
Follow these steps for free trial version.
Step 1: Click on “Trial Download” on the website.
After downloading and installation, a pop up like this would appear on your screen. Choose the option Request evaluation license for activation of a 14 day trial period.
Step 2: Select the Direct download option
Step 3: Click on next and license is downloaded
Step 4: Fill your details to get registered
You can read our reviews on other bioinformatics software
The software is really good as far as the accurate analysis results are concerned. Some of the advantages of the Workbench are:
- Performs most of the basic and general analysis
- It is fast in producing results
- Most of the advanced researches can be executed too such as molecular cloning and editing
- The secondary structure of RNA can be predicted
- 3D visualization of molecular structures is feasible
- Evolutionary relationships can be drawn for multiple sequences
- Gene Expression Analysis can be performed
- Sequence alignment, editing, and annotation
- Sharing of files among multiple users is possible
- User-friendly and intuitive user interface
- Tutorial videos for step by step guide
- Not costly. Affordable by individual scientific research scholars
Although there are too many advantages of QIAGEN CLC Main Workbench, there are some disadvantages too such as:
- The technicalities associated with using the tools can trouble the user
- The trial period may give access to only a few analysis tools but not all
- More advanced analysis like NGS and Sanger sequencing is not available
- Too slow if you choose the “accurate results” option
The technical requirements for the QIAGEN CLC Main Workbench are very detailed. Here I shall cover most of the requirements that would help you in running the software smoothly.
Basic information: QIAGEN CLC Workbench has been built with Java technology. For Windows, Mac OS X, or Linux users, QIAGEN CLC Workbench comes along JRE (Java Runtime Environment) that is needed for running the QIAGEN CLC Workbench uninterrupted.
If your system already has JRE there is nothing to be bothered about. The JRE embedded with the software does not interfere with the JRE on your computer. It is only used when you use the QIAGEN CLC Workbench.
- Windows 7, Windows 8, Windows 10, Windows Server 2012, Windows Server 2016, and Windows Server 2019 are compatible.
- Mac Operating System X 10.11 and above versions are compatible.
- Linux, RHEL 7 and later, SUSE Linux Enterprise Server 12, and more. To run the BLAST facility, libnsl.so.1 would also be needed.
- 64-bit Operating system with 1 GB RAM and 1024 * 768 display is mandatory. However, it is better to use 2 GB RAM and 1600 * 1200 display.
- A Graphics card that supports OpenGL 2.0 is needed for the 3D Molecular Viewer system.
- Updated graphics drivers and the latest graphics card should be installed.
Note: The different products of QIAGEN such as CLC Genomics Workbench and others have different technical requirements.
The splendid user experience comes from a fabulous user interface. The CLC Main Workbench is simple and easy to use. The main domains of the user area include:
- Menu bar: On the topmost left side of the page. Many actions related to the tasks can be found here.
- Toolbar: Top left side of the page. It includes all the tools related to the analysis.
- Status bar: Top left side of the page. It displays the status of Workbench and connection with other systems.
- Toolbox Area: On the bottom left area of the page. It consists of three tabs- Processes (list of tasks accomplished and pending), Toolbox (the list of workflows and analysis tools), and Favorites (most used tools are listed here).
- Navigation Area: On the top left side of the page. The data elements saved in file locations are listed here.
- View Area: On the right side of the page. It is spacious. It displays the work you are doing. Various ways of viewing are available. The selected tab at the top of the View Area shows the type of viewing active.
- Workspace: While working on a project, you may view it in different ways. You might want to save this arrangement of viewing, it is called Workspaces. You can switch between different workspaces.
- Workspaces are saved automatically when you close the Main Workbench. You can create, select, and delete the Workspace.
User Preferences and Settings Control
One of the key highlights feature why user experience is so wonderful on CLC Main Workbench is User Preferences and settings control. With the preferences option, you can change the default settings as per your convenience. It includes General preferences, View preferences, Data preferences, and advanced settings.
In addition to these four, there are two more settings that you can edit, namely Export/import of preferences and View settings for the Side Panel.
- The technical team of the QIAGEN CLC Main Workbench supports the users extensively. The customer care unit is supportive of availability through phone calls. You can email them to send the queries too.
- The user manual in PDF format and online mode is available for users to understand the application.
Limitations of The Software
Most of the features embedded in QIAGEN CLC Main Workbench are appropriate to carry out the entire analysis of sequences. Structures and phylogenetic relations can be traced too. However, it lacks one important aspect of analysis, which is NGS technology.
- Next-Generation Sequencing is one of its kind. It is the basis of most of the disease detection scientific researches. The genetic basis of any ailment can be identified by it. In today’s time, most of the work lies around the NGS.
- It does not provide tools for drug detection. Auto-dock and simulations are not provided here. An extension in protein analysis would have been great.
This QIAGEN CLC Main Workbench review includes all the functional aspects of the software. I feel content with what if offers. The results and performance are satisfactory.
I would recommend you to use QIAGEN CLC Main Workbench for total analysis even after the trial phase gets over. The added advantage of using the software is that it allows easy development of plug-ins for all the workbenches via an open API. You can use your plug-ins or the plug-ins developed by third parties.
Above all, being a student and affording commercial software is not easy. The price of the software is so genuine that any organization or individual can use it. Under the student license, any organization can buy it. This advantage works in favor of the users.
Frequently Asked Questions
Is there a trial version for QIAGEN CLC Main Workbench?
Yes, there is a trial version available.
Is the trial version free?
Yes absolutely. You can use it for 14 days without paying any single penny.
Is it compatible with Linux OS?
It is compatible with Windows, Mac, and Linux OS. You can read the Technical requirements section for details.
Can this be used for Docking and simulations?
No such tools are available at the present times. However, such an analysis can be integrated in the future.