CLC Main Workbench 5.5

• Assembly of DNA sequencing data
• Advanced primer design
• Molecular cloning
• Fully integrated 1D DNA Gel Simulator
• Automatic SNP annotation of sequences
• Secondary protein structure prediction
• Integrated 3D molecular view
• Signal Peptide Prediction (SignalP)
• Transmembrane helix prediction (TMHMM)
• Protein family analysis (PFAM)
• 2 types of alignments
• Phylogenetics
• Motif search (known patterns)
• Motif search using regular expressions
• Motif search using ProSite patterns
• Pattern discovery (unknown patterns)
• Web based BLAST
• BLAST on local databases
• Batch processing of multiple analyses in one work-step
• Dot plots
• Hydrophobicity analyses
• Antigenicity analyses
• Searches on GenBank, SwissProt, TrEMBL, and PubMed
• Detailed log of actions/analyses performed

1. Expression analysis including digital gene expression
   • Support for both microarray- and sequencing-based (RNA-Seq) expression data
   • Visualization: Interactive heat map, table and scatter plot views
   • Transformation and normalization tools
   • Quality control tools including principal component analysis, MA- and boxplots
   • Experimental design tools for two- or multiple group comparisons
   • T-tests and ANOVA analysis with support for paired/repeated measures
   • Multiple testing corrected p-values (Bonferroni and/or FDR)
   • Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
   • Ability to import NetAffx annotation arrays and adding annotation to experiments
   • Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. 'GO'stats or specific protein pathways).
   • Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
2. 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
3. RNA structure analysis
   • Secondary structure prediction
   • Graphical view and editing of secondary structure
   • Tabular view of structures and energy contributions
   • Symbolic representation in sequence view
4. 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
5. 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)
6. 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
7. 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

Enhancements:

• Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones.
• Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments.
• In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu.
• Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments.
• Bug fixes: Various bug fixes