15-11-2006

CLC bio New Hardware Accelerator

CLCbio have created the ‘CUBE’. A hardware unit which runs Smith Waterman up to 125 times faster than a 3 GHz desktop computer.

Using the Cube instead of BLAST, improves the quality of the data you're working with! read more..

CLC bio Protein Workbench

In addition to all the features in CLC Free Workbench, CLC Protein Workbench includes:

Bioinformatics features in Protein Workbench

3D molecule view
Transmembrame helix prediction
Antigenicity
Secondary protein structure prediction
PFAM domain search
Web-based prediction of signal peptides and their cleavage sites (SignalP - the best tool available)
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
Integrated UniProt searches (Swiss-Prot/TrEMBL)
Web-based lookup of sequence data in the UniProt and NCBI databases, as well as Google

Other Bioinformatics features

DNA, RNA and protein sequence editor displaying both linear and circular molecules
DNA, RNA, and protein alignment editor
Interactive logos along both DNA, RNA and Protein alignments
Batch processing of analyses on multiple sequences in one work-step
Motif search
Pattern discovery (unknown patterns)
Advanced re-alignment and fix-point alignment option
Sequence logo graphs along DNA, RNA, and protein alignments
Manual annotation of sequences
Integrated PubMed searches
Web-based sequence search using BLAST
Dot plot based analyses
Local complexity region analyses and complexity plots
Gap fraction graphs
G/C content analysis and graphs

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
Import of trace data files and quality scores from automated DNA sequening machines using Standard Chromatogram Format, ABI formats and PHD format (PHRED)

Viewing and reporting