CLC Main Workbench is an useful program that aggregates all features of CLC Free Workbench, CLC Protein Workbench, and CLC Gene Workbench in one integrated software package.

CLC Main Workbench creates a software environment enabling users to make a large number of advanced protein sequence analyses, combined with smooth data management, and excellent graphical viewing and output options.

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

· 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
· Import of trace data files and quality scores from automated DNA sequening machines using Standard Chromatogram Format, ABI formats and PHD format (PHRED)
· 3D molecule view
· Transmembrame helix prediction
· Antigenicity
· Secondary protein structure prediction
· PFAM domain search
· Web-based prediction of signal peptides and their cleavage sites (SignalP - the best tool available)
· 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
· Integrated UniProt searches (Swiss-Prot/TrEMBL)
· Web-based lookup of sequence data in the UniProt and NCBI databases, as well as Google
· Editor for graphically and algorithmically advanced primer design
· Assembly of DNA sequence data
· Molecular cloning
· Automatic SNP annotation of sequences
· Search and discovery of DNA patterns
· 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
· Short form DNA statistics including a number of characteristics of a given molecule
· NCBI sequence data search
· Access to web info from PubMed
· DNA, RNA and protein sequence editor displaying both linear and circular molecules
· DNA, RNA, and protein alignment editor
· Interactive logos along both DNA, RNA and Protein alignments
· Batch processing of analyses on multiple sequences in one work-step
· Motif search
· Pattern discovery (unknown patterns)
· Advanced re-alignment and fix-point alignment option
· Sequence logo graphs along DNA, RNA, and protein alignments
· Manual annotation of sequences
· Integrated PubMed searches
· Web-based sequence search using BLAST
· Dot plot based analyses
· Local complexity region analyses and complexity plots
· Gap fraction graphs
· G/C content analysis and graphs
· Advanced BLAST view
· Advanced graphs view
· Advanced histogram view
· Advanced dot plot view
· Search for characteristics in sequences and alignments

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

Limitations:

· 30 days trial

What's New in This Release: [ read full changelog ]

· Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones.
· Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments.
· In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu.
· Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments.