CLC Main Workbench

Category Cross-Omics>Sequence Analysis/Tools

Abstract CLC Main Workbench creates a software environment enabling users to make a large number of advanced protein, DNA, and RNA sequence analysis, combined with smooth data management, and excellent graphical viewing and output options.

Note: this product replaces "CLC Combined Workbench."

CLC Main Workbench includes all features and functions of CLC Protein Workbench, and CLC DNA Workbench, and CLC RNA Workbench.

Product features a number of unique and innovative bioinformatics tools for supporting advanced biochemistry and molecular biology lab research.

CLC Main Workbench features/capabilities include:

RNA structure analysis --

1) Secondary structure prediction - uses a minimum free energy (MFE) approach to predicting RNA secondary structure.

2) Graphical view and editing of secondary structure.

3) Tabular view of structures and energy contributions - the table contains a hierarchical display of the elements in the structure with detailed information about each element's energy contribution.

4) Symbolic representation in sequence view - this is used to display a symbolic representation of the secondary structure along the sequence.

DNA sequence analysis --

1) Editor for graphically and algorithmically advanced primer design.

2) Assembly of DNA sequence data - DNA sequence reads can be imported trimmed and assembled from automated sequencing machines.

A number of different file formats such as e.g. .SCF, .ABI, and PHD files are supported.

3) Molecular cloning - offers graphically advanced in silico cloning and design of vectors for various purposes.

4) Automatic SNP annotation of sequences.

5) Local complexity region analyses - you can calculate local complexity for both DNA and protein sequences.

6) Reverse translation from protein to gene, based on translation tables from a number of species.

7) Advanced restriction enzyme analysis and management.

8) Dot plot based analyses - Dot plots provide an advanced visual comparison of two sequences.

Dot plots can also be used to compare two regions of similarity within a sequence of DNA or protein.

9) DNA statistics report including a number of characteristics of a given molecule.

10) National Center for Biotechnology Information (NCBI) sequence data search.

11) Access to web info from PubMed.

Protein sequence analysis --

1) Integrated 3D molecule viewer - the 3 dimensional structures of proteins can be viewed and navigated in the fully integrated 3D viewer tool.

In addition, 3D views can be exported to several types of graphics files for use in publications and reports, etc.

2) Trans-membrane helix prediction.

3) Antigenicity - helps to identify antigenic regions in protein sequences using two different methods.

4) Secondary protein structure prediction - can be used to predict Alpha- helices and Beta-sheets (strands) based on Hidden Markov Model (HMM) algorithms.

5) Local PFAM domain search.

6) Web-based prediction of signal peptides and their cleavage sites.

7) Hydrophobicity analyses and graphs.

8) Protein charge analysis and graphs.

9) Reverse translation from protein to gene (a number of translation tables).

10) Interactive translations of DNA and RNA to protein (both single sequences and alignments).

11) Proteolytic cleavage detection.

12) Report of protein statistics (one or more proteins in each report).

13) Comprehensive report including a range of protein analyses in one document.

Pattern search --

1) Search for sequence matches;

2) Motif search for basic patterns;

3) Motif search with regular expressions;

4) Motif search with PorSite patterns; and

5) Pattern discovery (unknown patterns) - applying the Pattern Discovery process helps identify unknown sequence patterns across single or multiple DNA and protein sequences.

The discovery method is based on advanced hidden Markov models. If the analysis is performed on several sequences at a time the method will search for patterns which are common between all the sequences.

Database searches --

1) Web-based sequence search using BLAST;

2) BLAST on local databases;

3) Build local BLAST databases;

4) GenBank Entrez searches;

5) UniProt searches (Swiss-Prot / TrEMBL);

6) PubMed lookup;

7) Web-based lookup in UniProt, NCBI, and Google; and

8) SNP annotation using BLAST.

Project and data management --

1) Full integration of input data, data management, calculation results, and data export.

2) Detailed history log.

3) All types of files can be saved in local projects and launched from this program.

4) Import and export of data in a large number of different file formats.

5) Option of working in several active workspaces at one time, enabling simultaneous work on multiple projects.

Other bioinformatics features --

1) DNA, RNA and protein sequence editor displaying both linear and circular molecules.

2) Multiple alignments of DNA, RNA, and proteins - Two proprietary algorithms are offered plus an additional alignment plug-in -

This extension (plug-in) allows for the use of five (5) other alignment methods which are otherwise Not distributed with the CLC Workbench.

The five different alignment methods included in this extension are: ClustalW, Muscle, T-Coffee, Kalign and Mafft.

3) Joining multiple alignments into one - joining several alignments into one can be used to construct "super-genes" for phylogenetic inference.

4) DNA, RNA, and protein alignment editor.

5) Interactive logo graphs along DNA, RNA, and protein alignments.

6) Batch processing of analyses on multiple sequences in one work- step.

7) Advanced re-alignment and fix-point alignment option.

8) Manual annotation of sequences.

9) Gap fraction graphs.

10) G/C content (or guanine-cytosine content) analysis and graphs.

11) Advanced pairwise comparison.

12) Extract annotations.

System Requirements

Full requirements.


Manufacturer Web Site CLC Main Workbench

Price Academic license US $985; Industrial license US $3,950

G6G Abstract Number 20096A

G6G Manufacturer Number 100520