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CLC DNA Workbench 5.7
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CLC Bio (tutti i prodotti) Lingua : Ing | S.O. : Win, Mac, Linux

An advanced workbench for DNA analysis
CLC DNA 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.

CLC DNA Workbench is available on Windows, Mac OS X, and Linux platforms.

 

These are the top five reasons to try CLC DNA Workbench
Product features

 

CLC DNA Workbench includes the following features:

DNA sequence analysis

Pattern search

Database searches

Project and data management

Other bioinformatics features
New Features

For the latest improvements please visit the CLC Bio WebSite...

Screenshots

All features shown in the screenshots below are available in CLC DNA Workbench. Click the thumbnails to access the extensive collection of screenshots of our Workbenches. Please note that all screenshots are available in Windows and Mac versions and selected ones also in Linux versions.

Primer design

The primer design functionality in the workbench offers the user an unprecedented level of graphical interaction during the primer selection process. Primers can be designed for various experimental settings, using both single sequences and alignments. In the primer editor the user can easily select regions to define primer sets and immediately view the properties of all primers using various levels of detail. When primer selection criteria, such as melting temperature and self-annealing values are adjusted, the effect can be immediately evaluated.

The integrated nature of the workbench makes it easy to design primers that span or cover a specific genetic element. Here the user has chosen to design primers that span a known genetic variation. Information concerning this variation is displayed in the shown tool tip. Primers are required to have a length between 18 and 20 nucleotides and each available primer is indicated by a dot. Green dots indicate primers which fulfill all the selection criteria and red dots indicate primers which fail to meet one or more of the selection criteria.

Trace files

CLC Gene Workbench allows you to import, view, edit and analyze results from automated sequencing machines. Here a sequencing read is opened for inspection. The color intensity of each of the four nucleotides is shown as a trace-graph under the called sequence, and the associated quality values are shown as shaded green boxes in the background of the graph, allowing the user to easily interpret and edit the data. Automated algorithms for “trimming” the trace data are also included. Furthermore, the integrated framework of the workbench allows the user to perform various analysis on the proposed sequence, such as the open reading frame prediction shown in the lower view. These again aid in the interpretation of the experimental data. Upon inspection and verifi cation sequencing reads can be assembled into contigs using state-of-the-art algorithms.

Contig assembly

Analysis of cutting enzymes can be carried out in a static or more dynamic way. Here is shown a double stranded DNA sequence with a selection of restriction enzymes cleaving it. Enzymes can be enabled/disabled instantly in the Side Panel allowing only enzymes of interes to be shown.

Manual annotation of sequences

It is possible to manually annotate sequences by a selecting a region on the sequence. Annotations can be selected from a large hierarchical structured feature list, which holds more that 150 types of annotations related to both DNA and protein sequences. Annotation can be changed or removed at any time.

BLAST search

BLAST similarity searches against the 'nr' database at NCBI. The BLAST search is tightly integrated into the CLC Protein Workbench which removes a lot of "copy and paste" work between the program and the BLAST webpage.

 

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Core software features
 Data management
 Printing and reporting
 Import and export
 History
 Batch processing
 Customize solutions

Next Gen. Sequencing
 Genomics
 Transcriptomics
 Epigenomics
Chromatin immunoprecipitation sequencing analysis
Peak finding and peak refinement
Graph and table of background distribution and false discovery rate
Peak table and annotations

 General NGS features

Other Bioinformatics features
 RNA secondary structure
 BLAST searches
 Other database searches
 Protein analyses
 Dot plots
 Primer design
 Assembly of Sanger sequencing data
Advanced contig assembly
Importing, viewing, and editing trace data
Trim sequences
Secondary peak calling
Assemble without use of reference sequence
Assemble to reference sequence
Assemble to an existing contig
Viewing contigs
Editing contigs
Tabular view of an assembled contig (easy data overview)

 Molecular cloning
 Virtual gel viewer
 Pattern discovery
 General sequence analyses
 Nucleotide analyses
 Sequence alignment
 Phylogenetic trees

System Requirements

System requirements for all workbenches from CLC bio

  • Mac OS X 10.4 or later (including Intel-based Macs)
  • Windows 2000, Windows XP, Windows Vista, or Windows 7
  • Linux: Redhat or SuSE
  • 256 MB RAM required
  • 2 GB RAM recommended
  • 1024 x 768 display recommended

Additional requirements for CLC Protein Workbench, CLC Main Workbench, & CLC Genomics Workbench

  • 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards)

Special requirements for CLC Genomics Workbench

  • Intel or AMD CPU required
  • 64 bit computer and operating system recommended for more than 2 GB RAM
  • Small data sets:
    Assembly and analysis of genomes up to 50 mega-bases and up to 10 mil. reads
    • 2 GB RAM required
    • 4 GB RAM recommended
  • Medium data sets:
    Assembly and analysis of larger genomes and up to 100 mil. reads
    • 8 GB RAM required
    • 16 GB RAM recommended
  • Large data sets:
    Assembly and analysis of larger genomes and more than 100 mil. reads
    • 16 GB RAM required
    • 32 GB RAM recommended
  • Special requirements for de novo assembly:
    De novo assembly may need more memory than stated above - this depends both on the number of reads and the complexity and size of the genome. See our white paper on de novo assembly for examples of the memory usage of various data sets.

System requirements for CLC License Server

  • Mac OS X 10.4 or Mac OS X 10.5
  • Windows XP, Windows Vista, Windows 7 or Server 2003
  • Linux: Red Hat, Fedora Core or SuSE

Java

The CLC Workbenches are built using Java technology. If you are a Windows or Linux user, the CLC Workbench includes a JRE (Java Runtime Environment) which is needed to run the CLC Workbench. This JRE will not interfere with existing JRE's on your computer and will only be used to run the CLC Workbench.

Mac OS X includes a Java Runtime Environment as default.

Mac and the Mac logo are trademarks of Apple Computer, Inc., registered in the U.S. and other countries. Microsoft, Windows and the Windows logo are either registered trademarks or trademarks of Microsoft Corporation in the United States and other countries.

 
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