Main Workbench includes all features from CLC DNA Workbench, CLC RNA Workbench, and CLC Protein Workbench, as well as a range of Gene Expression Analysis - all listed below:

Expression analysis including digital gene expression

• 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

DNA sequence analysis

• 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

RNA structure analysis

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

Protein sequence analysis

• 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

Pattern search

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

Database searches

• 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

Project and data management

• 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

Other bioinformatics features

• 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