CLC DNA Workbench includes the following features:

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

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)

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

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

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