Author Topic: CLC Sequence Viewer Bioinformatics analyses and data management for OS X 10.4  (Read 2868 times)

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Software Santa

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CLC Sequence Viewer is Bioinformatics analysis and data management for OS X 10.4 or Later.

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

   1. You will have easy access to a large number of integrated research tools:
          * Creating and editing alignments
          * Interactive restriction site analysis
          * Phylogenetics
          * Integrated GenBank searches
          * Advanced DNA to Protein translation
          * And many more
   2. You can get easy access to hardware accelerated database searches
          * Plug in the Bioinformatics Cube and increase your search speed up to 200 times
   3. Your research work will be easy to carry out
          * The program is graphically based, intuitive, and user-friendly
   4. You will have a bioinformatics solution that continuously evolves
          * The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
   5. You will get superior customer service
          * We offer free support to all users - also users of our free demo version

Product features:

Bioinformatics features in CLC Sequence Viewer

    * Multiple alignment of DNA, RNA, and proteins
          o Two proprietary algorithms
          o ClustalW
          o Muscle
          o T-Coffee
          o MAFFT
          o Kalign
    * Consensus sequence determination and management
    * Conservation score along alignments
    * Open reading frame determination
    * Easy access to web-based protein and nucleotide search in GenBank, including download facilities and full graphical overview of sequence annotations of your choice
    * Translation from DNA to proteins (all genetic translation tables)
    * Reports with residue composition, molecular weight and iso electric point (for proteins)
    * Neighbor-joining and UPGMA phylogenies
    * Restriction site analysis and viewing
    * Create reverse complement
    * Shuffle sequence
    * Option of viewing and graphical manipulation of bioinformatics analyses made in commercial workbenches from CLC bio

Other features in CLC Sequence Viewer

    * Full integration of data input, data management, calculations results, and data export. This eliminates time spent on manual data transfers between different programs and databases
    * All types of files can be saved in local projects and launched from the program
    * Detailed history log
    * User-friendly graphical tools used in order to find and work with relevant regions of DNA, RNA and protein sequences
    * Text-based sequence view
    * Easy printing of reports and graphics
    * Export of user-defined figures to various graphics file formats
    * Import and export of data in a large number of file formats
    * Option of working with different files and in different file projects at the same time
    * Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects

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.

File formats:

File type    Suffix    File format used for
ACE files    .ace    contigs (only import)
Phylip Alignment    .phy    alignments
GCG Alignment    .msf    alignments
Clustal Alignment    .aln    alignments
Newick    .nwk    trees
FASTA    .fsa/.fasta    sequences
GenBank    .gbk/.gb/.gp    sequences
GCG sequence    .gcg    sequences (only import)
PIR (NBRF)    .pir    sequences (only import)
Staden    .sdn    sequences (only import)
DNAstrider    .str/.strider    sequences
Swiss-Prot    .swp    protein sequences
Lasergene sequence    .pro    protein sequence (only import)
Lasergene sequence    .seq    nucleotide sequence (only import)
Embl    .embl    nucleotide sequences
Nexus    .nxs/.nexus    sequences, trees, alignments, and sequence lists
CLC    .clc    sequences, trees, alignments, reports, etc.
Text    .txt    all data in a textual format
CSV    .csv    tables, each cell separated with semicolons (only export)
ABI    .abi    trace files (only import)
AB1    .ab1    trace files (only import)
SCF2    .scf    trace files (only import)
SCF3    .scf    trace files (only import)
Phred    .phd    trace files (only import)
mmCIF    .cif    structure (only import)
PDB    .pdb    structure (only import)
BLAST Database    .phr/.nhr    BLAST database (import)
Vector NTi Database         sequences (import of whole database)
VectorNTI achieves    .ma4/.pa4/.oa4    sequences (only import)
Gene Construction Kit    .gcc    sequences (only import)
RNA Structure    .ct/.col/.rnaml/.xml    RNA structures
Preferences    .cpf    CLC preferences

I believe this requires free registration. Santa frowns on programs that require you to do more than download and play but this is the only sequence reader he features. Hey - if you know what this is and you need it I'm sure you won't mind registration.


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