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CLC Sequence Viewer 6.4
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CLC Bio (tutti i prodotti) Lingua : Ing | S.O. : Win, Mac, Linux

A Sequence Viewer for basic bioinformatics

CLC Sequence Viewer creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.

The software package is a community edition, available for Windows, Mac OS X, and Linux. Download is free of charge.

These are the top five reasons to try CLC Sequence Viewer

Handling of different file formats

CLC Sequence Viewer is very versatile when it comes to importing and exporting both data and graphics files. To name a few, you can export graphics as PNG, PDF, or EPS. Import data from Vector NTI, CLUSTAL W, or DNA Strider. And among others GenBank, Fasta, Swiss-Prot, UniProt and EMBL formats are supported for both im- and export.

Click here to read the complete list of formats that are supported in CLC Sequence Viewer, and all other workbenches from CLC bio.

Product features

Bioinformatics features in CLC Sequence Viewer

Other features in CLC Sequence Viewer


New Features

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

 

Screenshots

All features shown in the screenshots below are available in CLC Sequence Viewer. 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.

Multiple sequence alignments

Powerful coloring and editing capabilities for multible sequence alignments. When the alignment is edited and colored the desired way it can be exported in different graphic formats to be used in reports and presentations.

Alignments and phylogenetic trees

Different views can be opened at the same time. Here is shown a multible sequence alignment and the corresponding phylogenetic tree both present and editable in the workbench.

Sequence statistics

Statistics can be shown for multible sequences in a comparative layout, thus it is easy to get an overview of differences in a number of DNA or protein sequences.

Restriction enzymes

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.

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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
 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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