CLC Main Workbench 6.5

CLC Main Workbench 6.5

User Rating: Fair (0.00/5)

Insustrial : $3950 / Academic : $985
RedHat 5 or later. SuSE 10 or later
January 30th, 2012

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CLC Main Workbench 6.5 Description

CLC Main Workbench 6.5 is made to be a smart and proper program which aggregates user friendly gene expression analysis with all features of CLC Protein Workbench, CLC RNA Workbench, and CLC DNA Workbench in one integrated software package.

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

Major Features:
  1. Expression analysis including digital gene expression:
    • Support for both microarray- and sequencing-based (post-mapping RNA-Seq) expression data
    • Visualization: Interactive heat map
    • Visualization: Scatter plots
    • Transformation and normalization tools
    • Quality control tools including principal component analysis, MA- and box plots
    • 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
    • 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
    • Multi-Site Gateway Cloning
    • 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
  2. DNA sequence analysis:
    • Secondary structure prediction
    • Graphical view and editing of secondary structure
    • Tabular view of structures and energy contributions
    • Symbolic representation in sequence view
  3. RNA structure 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
    • 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
  4. Protein sequence analysis:
    • Search for sequence matches
    • Motif search for basic patterns
    • Motif search using regular expressions
    • Motif search with ProSite patterns
    • Pattern discovery (unknown patterns)
  5. Pattern search:
    • 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
  6. Database searches:
    • 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
  7. Project and data management:
    • DNA, RNA and protein sequence editor displaying both linear and circular molecules
    • Multiple alignment of DNA, RNA, and proteins 
      • Two proprietary algorithms
      • ClustalW
      • Muscle
    • 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
  8. Other bioinformatics features:
  • New plug-ins and plug-in updates
    • MLST module updated
      • Possible to download MLST schemes from any web site compatible with mlstDBnet
      • When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than "New allele"
  • New and improved features
    • Multi-site Gateway Cloning. You can perform multi-site gateway cloning and in a few clicks create your expression clones with multiple fragments. The existing Gateway Cloning tool has been expanded so that you can easily recombine several fragments as well as continue using it for the standard Gateway Cloning.
    • Process tagged sequences
      • A summary report is now available with an overview of the number of reads per bar code.
      • You can search for barcodes (MIDs) on both strands, supporting new 454 protocol.
    • Find Binding Sites and Create Fragments improved:
      • If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G).
      • Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table).
    • Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.
  • Bug fixes
    • Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line.
    • Fixed: Set-up experiment would crash when using many samples.
    • Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. 
    • Fixed: importing adapters for trimming and barcodes for de-multiplexing did not work properly for CSV files and empty rows in Excel files were not allowed.
    • Fixed: Motif search did not exclude regions with Ns when the option "Exclude matches in N-regions for simple motifs" was selected.
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