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CLC Protein Workbench 5.4
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CLC Bio (tutti i prodotti) Lingua : Ing | S.O. : Win, Mac, Linux

An advanced workbench for protein analysis
CLC Protein Workbench creates a software environment enabling users to make a large number of advanced protein sequence analyses, combined with smooth data management, and excellent graphical viewing and output options.

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

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

 

CLC Protein Workbench includes the following features:

Protein sequence analysis

Database searches

Pattern search

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 Protein 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.

Protein charge graph of multiple sequences

Four proteins are included in the calculation of the protein charge on a varying pH scale. Coloring and presentation of the lines can be adjusted individually allowing great flexibility.

Kyte-Doolittle hydrophobicity calculation

Hydrophobicity calculations can help to identify transmembrane regions, antigenic regions and more, dependent on the hydrophobicity scale used.

Dotplot

Dotplots used for identifying repetitive regions or domains in two related sequences. You can zoom to single amino acid level in order to make detailed analyses. Gradients can be modified in the preference panel to the right.

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.

Alignment with shown annotations

Contrary to other alignment programs, CLC Protein Workbench allows you to show the annotations of the individual sequences in a multiple sequence alignment. This can easily identify whether certain domains are very conserved throughout an alignment. Moreover the information content of the individual columns in the alignment can be shown in form of a sequence logo, which can show information on highly conserved regions. The conservation of the individual residues in the alignments is shown as a histogram below the alignment.

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.

UniProt search

Search directly in the Swiss-Prot and TrEMBL databases from within the workbench. Swiss-Prot contains high quality data which have undergone manual curation and TrEMBL is computational annotated database. Various search parameter can be adjusted so queries only report an accurate result.

3D structure viewer

CLC Protein Workbench include an integrated 3D structure viewer. All protein specific analyses can be applied to the protein sequence of the structure.

 

 

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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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