CLC Main Workbench 5.1

CLC Main Workbench 5.1 is a powerful utility which aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench.

All analyses are fully integrated in one single, user-friendly, and intuitive software application.

Major Features:

1. 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
2. DNA sequence analysis
   • Editor for graphically and algorithmically advanced primer design
   • Assembly of DNA sequence data
   • Multiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.
   • Molecular 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
3. 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
4. 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
5. 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)
6. 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
7. 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
8. 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

Enhancements:

• Data generated with version 5.1 cannot be read in earlier versions
• Implementations of statistical tests for comparing expression levels of count-based expression measures as may be produced in RNA-seq
• • Kal's test for differences of proportions in single sample to single sample comparisons.
  • Baggerley's test for differences of proportions in two groups with replicates comparisons.
• "Reverse Contig" has been renamed to "Reverse Complement Contig." Functionality is un-changed.
• Exporting coverage graph to csv file now has an option to include or exclude gaps. Excluding gaps will make the file use the reference sequence coordinates
• Import of Illumina expression bead arrays and bead array annotation files
• Import of Affymetrix Chp files (CHP / PSI)
• Transformation of expression values now supports square root transformation.
• Better feedback on processes: there is a tool tip showing details and start time.
• Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
• Much improved memory performance and processing time of large data sets
• Improved performance when handling trace data. Trace now take up 50 % less disk space. This means that the data is opened and saved much faster and less memory is used.
• Output and error log files are now placed in the application data directory in the user home
• Fixed error when parsing files from Clone Manager (cm5-files)
• UniProt search works again
  

Requirements:

• Mac OS X 10.4 or later (including Intel-based Macs)
• Windows 2000, Windows XP, or Windows Vista
• Linux: Redhat or SuSE
• 256 MB RAM required
• 2 GB RAM recommended
• 1024 x 768 display recommended
• 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards)