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CLC Combined Workbench

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CLC Combined Workbench 2.1 is bioinformatics software developed by CLC bio A/S.
CLC Combined 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 Combined Workbench is available on Linux, Mac OS X, and Windows platforms.

Here are some key features of "CLC Combined Workbench":
Project and data management

Full integration of data input, data management, calculation results, and data export
Detailed history log
All types of files can be saved in local projects, and launched from the program
Import and export of data in a large number of file formats
Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
Import of trace data files and quality scores from automated DNA sequening machines using Standard Chromatogram Format, ABI formats and PHD format (PHRED)

Bioinformatics features in Protein Workbench

Alpha-helices and beta-sheets shown as annotations on the sequence.
3D molecule view
Transmembrame helix prediction
Antigenicity
Secondary protein structure prediction
PFAM domain search
Web-based prediction of signal peptides and their cleavage sites (SignalP - the best tool available)
Hydrophobicity analyses and graphs
Protein charge analysis and graphs
Reverse translation from protein to gene (a number of translation tables)
Interactive translations of DNA and RNA to protein (both single sequences and alignments)
Proteolytic cleavage detection
Report of protein statistics (one or more proteins in each report)
Comprehensive report including a range of protein analyses in one document
Integrated UniProt searches (Swiss-Prot/TrEMBL)
Web-based lookup of sequence data in the UniProt and NCBI databases, as well as Google

Bioinformatics features in Gene Workbench

Flexible viewing of circular molecules.
Editor for graphically and algorithmically advanced primer design
Assembly of DNA sequence data
Molecular cloning
Automatic SNP annotation of sequences
Search and discovery of DNA patterns
Local complexity region analyses
Reverse translation from protein to gene, based on translation tables from a number of species
Advanced restriction enzyme analysis and management
Dot plot based analyses
Short form DNA statistics including a number of characteristics of a given molecule
NCBI sequence data search
Access to web info from PubMed

Other bioinformatics features

DNA, RNA and protein sequence editor displaying both linear and circular molecules
DNA, RNA, and protein alignment editor
Interactive logos along both DNA, RNA and Protein alignments
Batch processing of analyses on multiple sequences in one work-step
Motif search
Pattern discovery (unknown patterns)
Advanced re-alignment and fix-point alignment option
Sequence logo graphs along DNA, RNA, and protein alignments
Manual annotation of sequences
Integrated PubMed searches
Web-based sequence search using BLAST
Dot plot based analyses
Local complexity region analyses and complexity plots
Gap fraction graphs
G/C content analysis and graphs

Viewing and reporting

Advanced BLAST view
Advanced graphs view
Advanced histogram view
Advanced dot plot view
Search for characteristics in sequences and alignments

Requirements:
256 MB RAM required
512 MB RAM recommended
1024 x 768 display recommended

What's New in This Release:
Automatic annotation of raw sequences with SNPs, DIPs and other types of small scale variations.
Annotation is based on user-friendly BLAST against the dbSNP database.
Better secondary protein structure prediction.
Additional parameters have been included in melting temperature calculations (Primer design).
Improved 3D viewing of molecules; among others including simultanious viewing of sequence structures in 2D and 3D.
Greatly enhanced web based BLAST.
Longer sequences can be BLASTed, the graphical user interface is improved, and the subsequent handling of search results has been improved.
Automated design of primers and TaqMan probes.
Enhanced BLAST on local databases.
The graphical user interface is improved, and the
subsequent handling of search results has been improved significantly.
You can now save HMM models generated in the Pattern Discovery function (searching for unknown patterns) - this reduces time for future pattern discovery searched significantly.
Advanced and interactive view of four different kinds of pairwise sequence comparisons: Gaps, Differences,
Identity, Jukes Cantor distances.
This program is shareware, which means you can download and use CLC Combined Workbench 2.1 for free during 30-days trial period. After this period you gonna have to buy CLC Combined Workbench 2.1 software for $120.00 or uninstall the program. CLC Combined Workbench 2.1 supports different languages (including english). It works with Linux.

Downloading CLC Combined Workbench 2.1 will take several minutes if you use fast ADSL connection.

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