Here are some key features of "CLC Main Workbench":

· 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
· 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
· 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

Requirements:

· 256 MB RAM required
· 512 MB RAM recommended
· 1024x768 screen resolution
· Java Runtime Environment 1.4 or higher
· 3D viewing requires an OpenGL 3D graphics driver