CLC Main Workbench 5.2

CLC Main Workbench 5.2 is a flexible application that 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 Benefits:

• You will have easy access to a large number of integrated research tools:
• • Editor for graphically and algorithmically advanced primer design
  • Assembly of DNA sequence data
  • Molecular cloning
  • Advanced RNA structure prediction and editing
  • Integrated and advanced Gene Expression Analysis
  • Integrated 3D molecule view
  • Sharing of data among researchers
  • All actions performed are logged automatically for later review or printing
• You can make your computer a High Performance Computing center
• • Use CLC Bioinformatics Cell to accelerate HMMER, ClustalW, and Smith-Waterman
  • Use CLC NGS Cell to accelerate reference assembly and de novo assembly of Next Generation Sequencing data
  • Plug in the Bioinformatics Cube and increase your search speed up to 200 times
• Your research work will be easy to carry out
• • The program is graphically based, intuitive, and user-friendly
  • Share data with your colleagues using CLC Database Solution
• You will have a bioinformatics solution that continuously evolves
• • The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority. Click here to see the many improvements coming up all the time
• You can customize your workbench
• You have the possibility to customize your workbench through our Software Developer Kit

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
   • 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
3. 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)
4. 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
5. 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
6. 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:

• New features:
• • Create new contig from selection
  • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • Heat maps and clustering improved  
  • Annotating samples or experiments for expression analysis:
  • Extract sequences improvements
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
  • "Find" in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Export of annotations in GFF format (note that annotations with joined regions are not supported)
  • Export of sequence data in fastq format
  • Now possible to perform detailed manual editing of contigs with up to 100,000 reads
  • Improved performance when zooming large contigs displaying a coverage graph
• Bug fixes:
• • Microarray import: Fixed a bug that prevented import of expression data with white spaces in column names.
  • Problem when adding annotations to an Illumina array file
  • Fixed problems importing expression annotation files
  • Fixed tblastn numbering issue
  • Fixed problem with graphics export of contigs
  • Problem rendering scatter plots without lines
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Various bug-fixes