CLC Protein Workbench 5.2

CLC Protein Workbench 5.2 is designed for providing 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 Benefits:

• You will have easy access to a large number of integrated research tools:
• • Integrated 3D molecule view
  • Transmembrane helix prediction
  • Secondary protein structure predictions
  • Identification of protein domains through PFAM domain searches
  • Prediction of signal peptides and their cleavage sites  
  • Sharing of data among researchers
  • All actions performed are logged automatically for later review or printing
• You can make your computer a High-Performance Computing center
• • Use CLC Bioinformatics Cell to accelerate HMMER, ClustalW, and Smith-Waterman
  • Plug in the Bioinformatics Cube and increase your search speed up to 200 times
  • Your research work will be easy to carry out
  • The program is graphically based, intuitive, and user-friendly
  • Share data with your colleagues using CLC Database Solution
• 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.
• You can customize your workbench
• You have the possibility to customize your workbench through our Software Developer Kit.

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)
   • 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
4. 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:

• New features:
• • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
  • Advanced view of elements in a folder including batch editing.
  • Extract sequences improvements
  • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
  • "Find" in text view now accepts Enter as command to find the next hit
  • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
  • Export of annotations in GFF format (joined regions not supported)
• Bug fixes:
• • Fixed tblastn numbering issue
  • Problem rendering scatter plots without lines
  • DNA strider files could loose name upon import
  • Rare misplacement of annotations when editing very large sequences
  • Various bug-fixes