• Support for both microarray- and sequencing-based (RNA-Seq) expression data
• Visualization: Interactive heat map, table and scatter plot views
• Transformation and normalization tools
• Quality control tools including principal component analysis, MA- and boxplots
• 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) with support for various distance and linkage measures.
• Ability to import NetAffx annotation arrays and adding annotation to experiments
• 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).
• Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results

• Editor for graphically and algorithmically advanced primer design
• In silico PCR
• Assembly of DNA sequence data
• Multiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.
• Molecular cloning
• Gateway Cloning
• Automatic SNP annotation of sequences
• Local complexity region analyses
• Reverse translation from protein to gene, based on translation tables from a number of species
• Advanced restriction enzyme analysis and management
• Dot plot based analyses
• DNA statistics report including a number of characteristics of a given molecule
• NCBI sequence data search
• Access to web info from PubMed

• Secondary structure prediction
• Graphical view and editing of secondary structure
• Tabular view of structures and energy contributions
• Symbolic representation in sequence view

• Integrated 3D molecule view
• Transmembrane helix prediction
• Antigenicity
• Secondary protein structure prediction
• PFAM domain search
• Web-based prediction of signal peptides and their cleavage sites (SignalP located on http://www.cbs.dtu.dk/services/SignalP/)
• Hydrophobicity analyses and graphs
• Protein charge analysis and graphs
• Reverse translation from protein to gene (a number of translation tables)
• Interactive translations of DNA and RNA to protein (both single sequences and alignments)
• Proteolytic cleavage detection
• Report of protein statistics (one or more proteins in each report)
• Comprehensive report including a range of protein analyses in one document

• Search for sequence matches
• Motif search for basic patterns
• Motif search using regular expressions
• Motif search with ProSite patterns
• Pattern discovery (unknown patterns)

• Web-based sequence search using BLAST
• BLAST on local databases
• Build local BLAST databases
• GenBank Entrez searches
• UniProt searches (SwissProt/TrEMBL)
• PubMed lookup
• Web-based lookup in UniProt, NCBI, and Google
• SNP annotation using BLAST

• Full integration of data input, data management, calculation results, and data export
• Detailed history log
• All types of files can be saved in local projects, and launched from the program
• Import and export of data in a large number of file formats
• Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects

• DNA, RNA and protein sequence editor displaying both linear and circular molecules
• Multiple alignment of DNA, RNA, and proteins
  
  • Two proprietary algorithms
  • ClustalW
  • Muscle
  • T-Coffee
  • MAFFT
  • Kalign
• Joining multiple alignments into one
• DNA, RNA, and protein alignment editor
• Interactive logo graphs along both DNA, RNA and Protein alignments
• Batch processing of analyses on multiple sequences in one work-step
• Advanced re-alignment and fix-point alignment option
• Manual annotation of sequences
• Dot plot based analyses
• Local complexity region analyses and complexity plots
• Gap fraction graphs
• G/C content analysis and graphs
• Advanced pairwise comparison
• Extract annotations

All features shown in the screenshots below are available in CLC Main Workbench. Click the thumbnails to access the extensive collection of screenshots of our Workbenches. Please note that all screenshots are available in Windows and Mac versions and selected ones also in Linux versions.

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, using both single sequences and alignments. 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. Information concerning this variation is displayed in the shown tool tip. Primers are required to have a length between 18 and 20 nucleotides and each available primer is indicated by a dot. Green dots indicate primers which fulfill all the selection criteria and red dots indicate primers which fail to meet one or more of the selection criteria.

BLAST search

BLAST similarity searches against the 'nr' database at NCBI. The BLAST search is tightly integrated into the CLC Protein Workbench which removes a lot of "copy and paste" work between the program and the BLAST webpage.

Dotplot

Dotplots used for identifying repetitive regions or domains in two related sequences. You can zoom to single amino acid level in order to make detailed analyses. Gradients can be modified in the preference panel to the right.

UniProt search

Search directly in the Swiss-Prot and TrEMBL databases from within the workbench. Swiss-Prot contains high quality data which have undergone manual curation and TrEMBL is computational annotated database. Various search parameter can be adjusted so queries only report an accurate result.

3D structure viewer

CLC Protein Workbench include an integrated 3D structure viewer. All protein specific analyses can be applied to the protein sequence of the structure.

Multiple sequence alignments

Powerful coloring and editing capabilities for multible sequence alignments. When the alignment is edited and colored the desired way it can be exported in different graphic formats to be used in reports and presentations.