CLC DNA Workbench 5.1

CLC DNA Workbench 5.1 is a powerful utility which provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. 

Major Features:

1. DNA sequence analysis
   • Editor for graphically and algorithmically advanced primer design
   • Assembly of DNA sequence data
   • Multiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.
   • Molecular cloning
   • Automatic SNP annotation of sequences
   • 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
   • DNA statistics report including a number of characteristics of a given molecule
   • NCBI sequence data search
   • Access to web info from PubMed
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. 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
   • SNP annotation using BLAST
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:

• "Reverse Contig" has been renamed to "Reverse Complement Contig." Functionality is un-changed.
• 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.
• Exporting coverage graph to csv file now has an option to include or exclude gaps. Excluding gaps will make the file use the reference sequence coordinates
• Much improved memory performance and processing time of large data sets
• Improved performance when handling trace data. Trace now take up 50 % less disk space. This means that the data is opened and saved much faster and less memory is used.
• 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)