CLC DNA Workbench 5.7.1

CLC DNA Workbench 5.7.1 provides you with a reliable and valued software which helps you successfully create a large number of advanced DNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options. CLC DNA Workbench is available on Windows, Mac OS X, and Linux platforms.

Major Features:

1. DNA sequence analysis
   • Editor for graphically and algorithmically advanced primer design
   • In silico PCR
   • Assembly of DNA sequence data
   • Multiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.
   • Molecular cloning
   • Gateway 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

• Improvements:
• • Improved performance of table filtering. Removed limit on the number of rows that can be filtered.
  • Option to search for read names in contigs (and also sequence lists and BLAST results).
  • Improved performance of conflict table view of contigs.
  • Better layout of graphics export and printing of contigs results: reference and consensus sequence repeated to provide an orientation context on all pages.
• Bug-fixes:
• • Fixed error when opening tables generated by the Transfac plug-in and the primer search tool
  • Fixed problem updating preview in Gateway cloning dialog
  • Genbank export of annotations on the negative strand were not in the right order
  • Fixed problems regarding editing and viewing of contigs and alignments
  • Fixed memory and performance issues related to import of many sequences, eg. from ACE files.
  • Various minor bug fixes

• Mac OS X 10.4 or later (including Intel-based Macs)
• 256 MB RAM required
• 2 GB RAM recommended
• 1024 x 768 display recommended