CLC DNA Workbench
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Bioinformatics program for advanced DNA sequence analysis.   Demo ($1,975.00)
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While CLC DNA Workbench 6.5 is still available for download, it has been discontinued and replaced by CLC Main Workbench 6.6.2.

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

We invite you to try a fully functional demo of our program - the first four weeks are free of charge. All data created in the demo-period is fully accessible from CLC Free Workbench. Trying a fully functional
What's New
Version 6.5:

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"

See a list of all plug-ins here.

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: 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. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis.
  • 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.
Version 6.5:

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"
  • more...
Requirements
Intel/PPC, Mac OS X 10.5 or later



MacUpdate - CLC DNA Workbench



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Downloads:7,908
Version Downloads:544
Type:Education : Teaching Tools
License:Demo
Date:28 Nov 2011
Platform:PPC 64 / PPC 32 / Intel 64 / Intel 32 / OS X
Price: $1,975.00
Overall (Version 6.x):
Features:
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While CLC DNA Workbench 6.5 is still available for download, it has been discontinued and replaced by CLC Main Workbench 6.6.2.

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

We invite you to try a fully functional demo of our program - the first four weeks are free of charge. All data created in the demo-period is fully accessible from CLC Free Workbench. Trying a fully functional demo version of CLC Gene Workbench is therefore a perfect way to access advanced DNA sequence analyses in a short period of time - free of charge.

Some analyses are:
  • Assembly of DNA sequencing data
  • Graphically and algorithmically advanced primer design
  • Molecular cloning
  • Automatic SNP annotation of sequences
  • Two types of alignments
  • Phylogenetics
  • Motif search (known patterns)
  • Pattern discovery (unknown patterns)
  • BLAST
  • Batch processing of multiple analyses in one work-step
  • Dot plots
  • Hydrophobicity analyses
  • Searches on GenBank and PubMed
  • Detailed log of actions/analyses performed


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