CLC Main Workbench 5.7.0

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
o Two proprietary algorithms
o ClustalW
o Muscle
o T-Coffee
o MAFFT
o 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