CLC Protein Workbench 5.3
CLC Protein Workbench 5.3 Ranking & Summary
CLC Protein Workbench 5.3 description
CLC Protein Workbench 5.3 is a beneficial and easy to use tool which provides a wide range of advanced protein analysis, and is based on the same user-friendly and integrated software environment as CLC Free Workbench.
This 2 x 2 weeks of fully functional demo includes a vast amount of advanced protein sequence analysis - all analyses are integrated in one single user-friendly and intuitive software application.
- Protein sequence analysis
- Integrated 3D molecule view
- Transmembrane helix prediction
- 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
- 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
- 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)
- 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
- 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
- You can set a path to the default data location used when the Workbench starts for the first time. This is a feature to help system administrators control where new installations per default save their data. Read more...
- Support for removing tools accessing the internet (NCBI BLAST, update notifications etc).
- General import and export
- Support for import of complex regions from GFF files
- Export tables and reports in Excel format.
- Import section of user manual re-structured to provide better overview. Read more.... Expression data importers are now described in technical details in a separate section. Read more....
- You can now export multiple sequence lists in fasta format
- Forced import of zip files is now supported (it will force import the contents of the zip file)
- The standard import now accepts gzip and tar files as well as zip
- If a forced import fails, there will be more technical information about what went wrong, allowing you to identify bad formatting of the import files
- Both Genbank and gff importer now makes several attempts at naming genes that do not have a gene name. It will iteratively try the following qualifiers: "product", "locus_tag", "protein_id" and "transcript_id"
- When importing genbank files where the length stated does not match the actual sequence, a warning is shown but the sequence is accepted.
- When exporting in csv format, the Locale settings are used to determine whether comma or semi-colons should be used as delimiter (comma used for US locales)
- GFF plug-in has been updated to accept complex annotations
- Advanced retyping of annotations using the annotation table. Read more...
- Improved reporting of situations when a full disk prevents saving of data
- Downloading sequences using drag and drop from the search table no longer creates a "Downloading..." node in the folder. The download process can be monitored in the Processes tab.
- Extract Sequences moved from File menu to Toolbox-> General Sequence Analysis. Read more...
- Better progress feedback on various dialogs
- Fixed problem displaying the "Copying..." label when copying data and then updating the folder
- Fixed problem with naming of tabs. The fix means that on Windows and Linux unsaved data now gets a * rather than make the tab name bold and italics. (This has always been the behavior on Mac OS X).
- Mac OS X 10.4 or later (including Intel-based Macs)
- 256 MB RAM required
- 2 GB RAM recommended
- 1024 x 768 display recommended
- 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards)
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