CLC Combined Workbench 2.2.4

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Описание программы CLC Combined Workbench

CLC Combined Workbench creates a software environment enabling users to make a large number of advanced protein sequence analyses, combined with smooth data management, and excellent graphical viewing and output options.
CLC Combined Workbench is available on Linux, Mac OS X, and Windows platforms.

· Ключевые особенности и характеристики CLC Combined Workbench 2.2.4

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)

Bioinformatics features in Protein Workbench

· Alpha-helices and beta-sheets shown as annotations on the sequence.
· 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

Bioinformatics features in Gene Workbench

· Flexible viewing of circular molecules.
· Editor for graphically and algorithmically advanced primer design
· Assembly of DNA sequence data
· Molecular cloning
· Automatic SNP annotation of sequences
· Search and discovery of DNA patterns
· 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
· Short form DNA statistics including a number of characteristics of a given molecule
· NCBI sequence data search
· Access to web info from PubMed

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

Viewing and reporting

· Advanced BLAST view
· Advanced graphs view
· Advanced histogram view
· Advanced dot plot view
· Search for characteristics in sequences and alignments

· Ограничения CLC Combined Workbench 2.2.4

· Специальные требования CLC Combined Workbench 2.2.4

· 256 MB RAM required
· 512 MB RAM recommended
· 1024 x 768 display recommended

· История версий и изменений CLC Combined Workbench

· Import of VectorNTI database significantly improved
· Fixed a problem with SNP BLAST caused by a change at the NCBI server.
· Fixed error that occurred when trimming away user defined vector sequence.
· Fixed minor problem in displaying trace files of extremely poor quality.

· Описание и дополнения от редакторов и пользователей сайта

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