CLC Main Workbench 5.1

This 2 x 2 weeks of fully functional demo of CLC Main Workbench aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench.
CLC Main Workbench is a tool that integrates all analyzes in one single, user-friendly, and intuitive software application.

Main features:
- Assembly of DNA sequencing data.
- Advanced primer design.
- Molecular cloning.
- 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).
- Pattern discovery (unknown patterns).
- BLAST.
- 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.

System requirements:
- 256 MB RAM required.
- 512 MB RAM recommended.
- 1024 x 768 display recommended.

Version restrictions:
- 4 weeks fully functional trial period.

Enhancements
- Data formats: Data generated with version 5.1 cannot be read in earlier versions
New features:
- Implementations of statistical tests for comparing expression levels of count-based expression measures as may be produced in RNA-seq
- Kals test for differences of proportions in single sample to single sample comparisons.
- Baggerleys test for differences of proportions in two groups with replicates comparisons.
- "Reverse Contig" has been renamed to "Reverse Complement Contig." Functionality is un-changed.
- 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
- Import of Illumina expression bead arrays and bead array annotation files
- Import of Affymetrix Chp files (CHP / PSI)
- Transformation of expression values now supports square root transformation.
- 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
- 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.
Bug fixes:
- Fixed error when parsing files from Clone Manager (cm5-files).
- UniProt search works again.