CLC RNA Workbench 4.1

CLC RNA Workbench 4.1 is a powerful utility which gives the user easy access to a range of complex algorithms and options. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms.

Major Features:

1. Bioinformatics features in CLC RNA Workbench
   • Secondary structure prediction
   • Graphical view and editing of secondary structure
   • Tabular view of structures and energy contributions
   • Symbolic representation in sequence view
2. 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)
3. 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 analyzes on multiple sequences in one work-step
   • Advanced re-alignment and fix-point alignment option
   • Manual annotation of sequences
   • Dot plot based analyzes
   • Local complexity region analyzes and complexity plots
   • Gap fraction graphs
   • G/C content analysis and graphs
   • Advanced pairwise comparison
   • Extract annotations
5. Database searches
   • Web based sequence search using BLAST
   • BLAST on local databases
   • Build local BLAST databases
   • GenBank Entrez searches
   • PubMed lookup
   • Web based lookup in UniProt, NCBI, and Google

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)

Requirements:

• 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