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CLC Combined Workbench Publisher Description

CLC Combined Workbench aggregates all features of CLC Free Workbench, CLC Protein Workbench, and CLC Gene Workbench in one integrated software package.

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.


OS: PPC/Intel
Requirements: Mac OS X 10.3 or later.
Whats new:
Version 3.0: The following has been updated: Highlights All the features of the CLC RNA Workbench are now included. Algortihms for free energy minimization based prediction of RNA secondary structure Advanced and fully integrated graphical editors for linear and 2D viewing and editing of RNA secondary structures. Advanced prediction of secondary structure using predefined constraints for base pairing. Table showing multiple secondary structures for one sequence Overview of each structure element's energy contribution Work directly on data on a shared network drive Improvements of annotation editing through the new annotation table. Copy and paste annotations from one sequence to another. New fragment table when doing restriction sites analysis. Secondary peak calling Translation of sequences in a contig improved (reading frames are aligned with consensus sequence, mutations on the amino acid level are shown in red - silent mutations are shown in yellow) New scales for graphs along the sequence (in the Side Panel when viewing protein sequences under "Protein Info"): Surface probability (Emini) Backbone chain flexibility (Karplus and Schulz) It is now possible to create a virtual gel simulating a restriction enzyme digest. PFAM domains now include a link to the PFAM website providing more detail about the domain. The link is available from the Annotation table. Full support for Windows Vista One-click switch between views (e.g. circular and linear sequences views) New annotation table - easy overview and filtering of annotations State-of-the-art layout of annotations Better and more intuitive handling of files (you can now access the files directly on the file system) It is now possible to "Save as" Easily expand selections using the mouse Improvements of restriction site analysis All the details Data handling It is possible to add new locations to the Navigation Area by clicking the "Add Location" icon in the small tool bar above the Navigation Area. This makes it possible to use any folder directly from within the Workbench. A folder on a shared network drive can also be used enabling sharing of data with other users. If more than one user tries to edit the same file, the second user who tries to save changes will be notified that the file has been changed. This user is then encouraged to use the "Save As" instead. Restriction sites New restriction map object created when doing restriction sites analysis. Restriction maps can be viewed as either fragment tables or virtual gels. Fragments in tables are displayed with graphical illustration of overhangs. When more than one enzyme cut at the same position, fragments are colored red to indicate that the result might differ in an in vitro experiment. Sequence views Possibility to specify own annotation types. The list of annotation types can now be expanded simply by typing the name of a new type. The Edit/Add Annotation dialog has been improved to make it possible to enter more information about an annotation. Following the conventions of the GenBank format, you can now add a number of qualifier/key pairs. You can add links to web sites on annotations. In the qualifier/key part of the annotation dialog, you can simply enter a URL (link) and it will be possible to click on the link in the annotation table and open a browser. More intuitive to edit alignments. Deleting and inserting gaps is now done for the selected sequences only. Deleting part of the sequence now moves the position of the rest of the sequence (instead of introducing gaps) For graphs along the sequence, you can now enter a custom window size. Previously it was restricted to a few options. BLAST In sequence views, you can make a selection, right-click and "BLAST Selection" both against NCBI and a local database. Selecting a row in the BLAST table make a corresponding selection in the graphical BLAST view Motif search Regions with N's are not searched when doing motif searches. Selecting a motif in a motif search table will make a corresponding selection in the sequence view. Primer design It is now possible to set a value for "Maximum pair end annealing" score In alignment-based primer design, it is now possible to specify a "No primers here" region like in the single-sequence primer design. It is available in the right-click menu on a selection. Assembly and sequencing data analysis It is now possible to assemble to a reference sequence with only one read. You can now right-click the name of a sequence in a contig and delete the sequence. Improvements of the contig table: conflicts are now kept in the table after they are resolved. A new field has been added to indicate status as "Resolved". Single-click editing of single bases is now also possible in normal sequence views (it was previously only possible in contigs). Secondary peak calling. In the Toolbox under "Sequencing Data Analysis", you find "Call Secondary Peak". It looks at the peaks in the sequence and is able to detect a "peak within a peak". This is useful when looking for heterozygous mutations. General use One-click switch between views (e.g. circular and linear sequences views). There is a new row of buttons at the bottom of each view which you can click to switch the view. Pressing Ctrl (Command on Mac) while clicking creates a split view of the two. Pressing Ctrl (Command on Mac) while rolling the scroll wheel of the mouse can now be used to zoom in and out (only possible for mice with scroll wheels). Many right-click menu items have now icons to make it easier to navigate the menus. Simplifying the task of creating a new sequence. Rarely-used elements like "Keywords" and "Comments" have been removed from the dialog, and the two steps have been merged into one. You can now use I (inosine) in nucleotide sequences. Better choices for the resolution of exported graphics. Sequence views Easily expand selections using the mouse. When you have made a selection, place the mouse cursor on the edge of the selection, and you can now adjust the selection. This is also possible for each part of a multiselection. Quick-jump to annotations. In the Side Panel under "Annotation types", it is now possible to click a quick-jump button which lets you go directly to the annotation. This provides a very quick and easy way of browsing annotations. The names of annotations are now repeated on each new line in a wrapped sequence view. The user can now specify which symbol to use in an alignment consensus sequence in case of ambiguities. In nucleotide sequence views, you can introduce a space for every three characters to visualize codons. In the Side Panel under "Sequence layout" there are now several options for "Spacing": Every 10 residues, every 3 residues in three reading frames. It is possible to search in text views. In the Side Panel, there now is a "Find" group where you can enter a text to search for. You can now hide labels in sequence views. This is particularly convenient with long sequence names taking up a lot of space. Import and export Pasting simple sequence text (like ATCGTACGTA) in the Navigation Area automatically creates a new sequence. Import and export of view settings (the settings saved in the Side Panel). In the Preferences dialog (available from the Edit menu), in the "View preferences" you can now export and import the View settings. All tables can be exported in a CSV format (semicolon-separated). When exporting sequences in this format, the annotations are exported. Restriction site analysis "Restriction Sites Analysis" has been renamed to "Create Restriction Map" and the dialogs are more intuitive to use. It is now possible to filter the list of enzymes to easily pick a specific enzyme. It is easier to set the number of cut sites for the restriction enzymes to be displayed When you open an enzyme list, you can select a number of enzymes, right-click and "Create New Enzyme List from Selection". This makes it easy to create subsets of enzyme lists. Combined with the table's filter, this makes it easy to extract e.g. restriction enzymes from a specific vendor. Data handling Copy an element in the Navigation Area by dragging while pressing the Ctrl button (Command button on Mac) Filter elements in the Navigation Area (to show e.g. only nucleotide sequences). The filter is available from the small tool bar above the Navigation Area. When selecting elements for analysis, only the relevant elements are shown (e.g. only nucleotide sequences are visible when selecting sequences for Restriction Site Analysis). When selecting elements for analyzes (in the select elements dialog), you can right-click a folder and add all the elements in that folder. Possible to sort elements alphabetically One-click renaming of elements. Simply click an element which is already selected, and you can type a new name directly. Recycle bin is now visible and you can easily restore deleted elements simply by dragging to the desired folder. In the File menu, there is a "Save As" menu item. It saves the opened element under a new name. Easily collapse all folders in the Navigation Area by clicking the "Collapse All" icon in the small tool bar above the Navigation Area. Plug-ins and licenses Plug-ins are now installed for all users of a computer. Licenses also apply to all users of the computer.

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