CLC Protein Workbench 5.1

CLC Protein Workbench 5.1 is a useful tool which provides a wide range of advanced protein analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench.

This 2 x 2 weeks of fully functional demo includes a vast amount of advanced protein sequence analyses - all analyses are integrated in one single user-friendly and intuitive software application.

Major Features:

1. 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
   • 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
2. 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
3. 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)
4. 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
5. 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

Enhancements:

• Better feedback on processes: there is a tool tip showing details and start time.
• Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
• Much improved memory performance and processing time of large data sets
• Output and error log files are now placed in the application data directory in the user home
• Fixed error when parsing files from Clone Manager (cm5-files)
• UniProt search works again

Requirements:

• 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards)
• Mac OS X 10.4 or later (including Intel-based Macs)
• Windows 2000, Windows XP, or Windows Vista
• Linux: Redhat or SuSE
• 256 MB RAM required
• 2 GB RAM recommended
• 1024 x 768 display recommended