CLC Protein Workbench provides a wide range of advanced protein analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench.
CLC Protein Workbench is a software solution for scientists and lab researchers working with biochemistry.
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 Main Workbench is available on Windows, Mac OS X, and Linux platforms.
Here are some key features of "CLC Protein Workbench":
Protein sequence analysis:
· Integrated 3D molecule view
· Transmembrane helix prediction
· Antigenicity
· Secondary protein structure prediction
· PFAM domain search
· Web-based prediction of signal peptides and their cleavage sites (SignalP located on http://www.cbs.dtu.dk/services/SignalP/)
· 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
Database searches:
· Web based sequence search using BLAST
· BLAST on local databases
· Build local BLAST databases
· GenBank Entrez searches
· UniProt searches (SwissProt/TrEMBL)
· PubMed lookup
· Web based lookup in UniProt, NCBI, and Google
Pattern search:
· Search for sequence matches
· Motif search for basic patterns
· Motif search using regular expressions
· Motif search with ProSite patterns
· Pattern discovery (unknown patterns)
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
Other bioinformatics features:
· DNA, RNA and protein sequence editor displaying both linear and circular molecules
· Multiple alignment of DNA, RNA, and proteins, Two proprietary algorithms, ClustalW, Muscle, T-Coffee, MAFFT, Kalign
· Joining multiple alignments into one
· DNA, RNA, and protein alignment editor
· Interactive logo graphs along both DNA, RNA and Protein alignments
· Batch processing of analyses on multiple sequences in one work-step
· Advanced re-alignment and fix-point alignment option
· Manual annotation of sequences
· Dot plot based analyses
· Local complexity region analyses and complexity plots
· Gap fraction graphs
· G/C content analysis and graphs
· Advanced pairwise comparison
· Extract annotations
Requirements:
· 256 MB RAM required.
· 512 MB RAM recommended.
· 1024 x 768 display recommended.
Limitations:
· 30 days trial
What's New in This Release: [ read full changelog ]
Minor improvements:
· Translate to protein creates sequence lists as results when more than 10 sequences are produced. This greatly improves performance when translating large amounts of proteins
· It is now possible to specify the number formatting in tables in the View Preferences.
Bug fixes:
· Fixed: Downloading of protein sequences from NCBI fails.
· Fixed: Opening external files (e.g. pdf files or Word documents) with spaces in the file name does not work on Windows.
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