CLC Protein Workbench 5.4

New features:

• Improved memory management in general: lower memory footprint and shorter management overhead pauses.
• Improved memory handling of large tabular data sets.
• Improved consistency of data handling including faster listing of folder contents
• Performance when saving small files significantly improved
• Sequence annotations are packed to lower memory footprint and disk space usage, especially for SNP, DIP, and Conflict annotations.
• Improved performance of reading data files from shared drives.
• BLAST: In the overview BLAST table, it is now possible to extract query sequences. Read more
• Folder structure (expanded/collapsed folders) is preserved through the life-time of a wizard (e.g. when selecting input data and reference for read mapping)
• Find in Side Panel: separators are allowed when performing position search (e.g. 1.000.000 or 1,000,000 or 1'000'000 or 1 000 000). Read more

Bug-fixes:

• Print of folder content now takes settings in the Side Panel into account
• Find in Side Panel: space are now allowed
• Genbank import: sequence name (LOCUS) was truncated to 18 characters

CLC Protein Workbench 5.3

New features

Bug-fixes:

• 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).

CLC Protein Workbench 5.2.0

New features:

• Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
• Advanced view of elements in a folder including batch editing.
• Extract sequences improvements
• You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
• "Find" in text view now accepts Enter as command to find the next hit
• Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
• Export of annotations in GFF format (joined regions not supported)

Bug fixes:

• Fixed tblastn numbering issue
• Problem rendering scatter plots without lines
• DNA strider files could loose name upon import
• Rare misplacement of annotations when editing very large sequences
• Various bug-fixes

This update is recommended for all users.

CLC Protein Workbench 5.1

New features:

• Better feedback on processes: there is a tool tip showing details and start time.
• Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
• Much improved memory performance and processing time of large data sets
• Output and error log files are now placed in the application data directory in the user home

Bug fixes:

• Fixed error when parsing files from Clone Manager (cm5-files)
• UniProt search works again

CLC Protein Workbench 5.0.2

Updates

• Better performance of files with many annotations
• Fixed error and improved performance of Join Sequences tool
• Various bug fixes

CLC Protein Workbench 5.0.1

Updates

• Find in the Side Panel did not support spaces when searching for annotations
• Sequence statistics codon count were not correct when using sequences
• Fixed error when exporting alignments in aln format

CLC Protein Workbench 5.0

Improved user experience of processes

• Non-modal feedback from processes:
  • When there is a message (e.g. from a BLAST search: not hits found)
  • If you have chosen to save the results in the last step of the wizard, you will be notified when the process is done.
  • Processes running on the CLC Science Server will notify when they are done.
• Possibility to open results by clicking the button next to the process
• Possibility to find and select results in the Navigation Area by clicking the button next to the process
• You can see a log of your process by clicking the button next to the process (even if you did not choose to see the log in the last step of the wizard)

3D editor re-design

• The 3D editor now allows you to select individual structure subunits, residues, active sites, disulfide bridges and even atoms, and to customize their appearance

General improvements

• Limited mode: when using a license server - if there are no more licenses left, you can still access your data. The Workbench will then run in Limited mode where only a few tools are available (corresponds to the tools found in CLC Sequence Viewer). Click "Limited Mode" in the license dialog.
• Tables:
  • New advanced filter to use numerical data for filtering and to combined several filter criteria. Click the small button next to the normal filter to see the advanced filter.
  • Visual feedback when sorting and filtering tables
  • Improved automatic detection of column width
• Performance of graphs and plots improved
• Local BLAST is upgraded to use NCBI BLAST version 2.2.19
• More elaborate error reports including error logs
• You can specify which folder the Workbench should use for temporary files
• Extract sequences from a sequence list, contig or alignment by right-clicking the white empty space. You will then be able to extract the sequences into a list or as separate sequences.
• The "Find" option in the Side Panel of sequence views automatically detects if you have entered a position instead of a sequence.

Plug-ins

• Extract Annotations plug-in has been improved:
  • Possibility to specify the naming of the sequences (based on annotation name, type etc)
  • Performance improvements to make it possible to extract annotations of large genomes.
• MLST plug-in: various bug fixes

Bug fixes

• Locale settings were not automatically set right on the first start-up. The locale settings determine whether . or , should be used for before decimals. For new installations of the Workbench, it will now be set to the locale of the computer's operating system. For existing installations, you will have to change this in the Edit->Preferences dialog.
• Fixed problem when BLASTing with an empty sequence
• Various performance improvements and bug fixes

CLC Protein Workbench 4.1.2

The following has been updated:

• The Side Panel's Find only high-lighted the first hit. This is now fixed.
• Extract sequences: fixed an error when extracting paired-ends sequences from contigs and sequence lists
• Local BLAST: solved problem applying command-line parameters, now a checkbox determines whether command-line options should take effect
• BLAST: it was possible to use a BLAST result as input and database
• Better performance when zooming a dot plot
• Better performance when using the Side Panel's Find in large contigs and sequence lists
• When right-clicking a CDS annotation and translating into protein, gaps were erroneously introduced into the protein sequence
• Multi-select (using Ctrl / Command key) did not work for sequence lists
• Various bug fixes

CLC Protein Workbench 4.1.1

The following has been updated:

• Fixed problems when scrolling very large sequences
• Fixed problem when importing very large GenBank files

CLC Protein Workbench 4.1

General performance improvements

• Improved performance when handling large data sets

• New plug-in! GFF/GTF support: You can now annotate a sequence using a GFF/GTF file. The plug-in is available for all Workbenches (not CLC Sequence Viewer). Once installed, you find it in Toolbox->General Sequence Analysis-> Annotate from GFF/GTF File. Read more...
• Extract annotations plug-in updated: it now uses the name of the annotation as the name of the new sequence.

• Various bug-fixes.

CLC Protein Workbench 4.0.1

New features

• Scrollbars can be adjusted manually

• Fixed problems when aligning sequences with lowercase characters
• Fixed import of trace files without quality scores
• Fixed problem when removing location
• A new sequence list can be created from a selection in the table view
• User definable scrollbar areas for contig views
• A few other minor bugs have been fixed.

CLC Protein Workbench 4.0

Performance improvements

• Support for data handling for larger sequence lists
• Import of larger sequence lists (fasta)
• View larger sequence lists
• Sequence views with annotations are rendered much faster

Licensing system

• More smooth system for handling licenses based on license order IDs
• Support for download of a license via web interface
• License server support for plug-ins
• User-friendly license wizard
• More reliable license system
• Easier to upgrade to newer versions

Tables

• Better correspondence between tables and sequence lists (e.g. selecting a row in the table high-lights the corresponding region on the relevant sequence)
• Number of selected rows in a table is now shown in the status bar
• Enzyme lists and restriction site tables now includes information about the length of the recognition sequence of the enzyme
• Create a new sequence list from selected sequences in the sequence list table (right-click the selected sequences)
• Support for copying from an enzyme list and pasting into a spreadsheet
• Fine-grained filtering of specific columns in a table

Views

• Alignments: possible to batch delete sequences
• Alignments: possible to toggle marked status of sequences
• Shift-clicking to extend selection also works on sequences with restriction sites
• The mouse cursor's position on the sequence is now shown in the status bar
• More fine-grained control when deleting annotations on multiple sequences
• Element info replaces the old "Sequence info" view and the "Properties" window. Undo-support and support for database-specific keywords.
• Improvement of scale layout of graphs

NCBI and UniProt search

• Results for searches includes information about the length of the sequence
• Ordering of search results makes it easier to add more results to the list

BLAST

• Local BLAST upgrade to 2.2.18
• NCBI BLAST uses the new server at NCBI
• The BLAST table includes information about the overlap

Miscellaneous

• Extract sequences works for large BLAST results, alignments, sequence lists and contigs
• Use an imported fasta file as motif list
• Better naming of primers when saving from primer table
• Motif search: the table now shows information about the length of a match
• Better correspondence between tables and sequence lists (e.g. selecting a row in the table high-lights the corresponding region on the relevant sequence)

CLC Protein Workbench 3.6.2

The following has been updated:

• BLAST of contigs no longer changes the contig name
• A few other minor bugs have been fixed.

CLC Protein Workbench 3.6.1

The following has been updated:

• Various bug-fixes
• It is now possible to include NCBI BLAST in protein report
• Fixed copy/paste errors in sequence list table
• Made it possible to Ctrl-doubleclick to extend selection between restriction sites
• Improved user interface for adding motifs to motif lists

CLC Protein Workbench 3.6

The following has been updated:

• Motif list search: It is now possible to do motif search using a list of motifs.
  • The list of motifs can be saved and exported
  • The list can contain different types of motifs: simple or regular expressions (Java or PROSITE)
• Multi request NCBI BLAST (up to 50 concurrent requests)
  • Makes it much faster to BLAST multiple sequences
  • Improved status messages when BLASTing multiple sequences
• Contigs (consensus sequence) fully supported by BLAST (both Local and NCBI)
• Extended BLAST table:
  • Shows if the hit is on the positive or negative strand
  • For tblastn, the reading frame for the hit is shown
  • The number of gaps, and gap percentage is shown
• BLAST overview table contains more information:
  • Shows hit with greatest percent identity
  • Shows hit with greatest percent positive
  • Shows longest hit
• Restriction sites available in Side Panel are computed up to 6 times faster
• Enzyme tables support "delete" via Tool bar and Delete key
• It is now possible to reverse a sequence. Available both in the Toolbox under Nucleotide Analysis and in the right-click menu in the Cloning Editor.
• Better focus system - it is now easier to see what part of the screen that has focus. An error in the focus system has also been corrected.
• Various bug fixes.

CLC Protein Workbench 3.5.1

The following has been updated:

• Organism name is now available in sequence list tables
• Fixed Mac problem when closing tabs
• Fixed minor issues and improved overall program stability
• Improved view layout of very long sequence labels
• Fixed stability issues related to the Recent Items plugin

CLC Protein Workbench 3.5

Framework

• Search
  • Full text search (quick search field)
    • Query guide system (Shift + F1 in search field)
    • Pressing Alt while clicking: locate data in Navigation Area
  • Full text search editor
    • Can be saved for quick search later on
  • Automatically updated search index of all data
• New floating license concept
  • Automatic license server detection
  • Advanced license borrowing enables off-line use of workbench
• New and improved plug-in and resource management
  • New user interface
  • Quick button in toolbar
  • New concept: Resources - PFAM databases can be downloaded for easy update
  • Better progress measurement during download, installation etc.
  • Automatic update check
  • Integrated plug-in registration: SignalP, TMHMM
• Automatic restart (after plug-in installation, exceeding of memory capacity and license changes)

Views

• Cut, copy, paste and delete actions work better in both sequence viewers and tables (no need to right-click any more)
• Position of annotations in alignments etc. now relative to both alignment and sequence
• Numeric scales now shown on graphs along sequence (hydroplots, coverage, conservation, sequence logo etc)
• Selecting a row in a table makes an interactive selection on the corresponding sequence (now implemented for all relevant tables)
• The Find functionality in the Side Panel has been improved to make it possible to search in sequences with ambiguity character e.g. Ns
• It is possible to open much larger sequence lists in the graphical view.

Restriction sites

• Side Panel re-design
  • Sorting of enzymes by alphabet, number of cuts or overhang type
  • Simpler management of enzymes
  • Improved tool tips on side panel enzymes showing recognition sequence and cleavage pattern
  • Quickjump to restriction sites
• Improved enzyme selection wizard
• Tool tips on restriction sites now include:
  • Methylation inhibition
  • Possible star activity (non-specific recognition and cleavage)
• Enzyme list table:
  • Information about possible star activity (non-specific recognition and cleavage)
  • New button: Add/Remove Enzymes
  • New button: Create new enzyme list from selection

BLAST

• Local "on-the-fly" BLAST (also Cube and Cell)
  • No need to build BLAST database aforehand
• Multi BLAST table - overview when blasting multiple input sequences(also Cube and Cell, NCBI BLAST, SNP BLAST)
• Possibility to use command line options in Local BLAST
• Hit length is shown in table view
• (Local) BLAST performance much improved for very large sequences

Miscellaneous

• Shuffle sequence includes more algorithms - now possible to shuffle while preserving di-nucleotide frequency
• Added codon frequency tables for: *Arthrobacter aurescens TC1 *Streptomyces coelicolor A3(2)
• Finding open reading frames: the table includes more information:
  • Strandedness
  • Nucleotides in the start codon
• It is now possible to extract all sequences from a sequence list, an alignment or a contig (File->Extract Sequences)
• Creating phylogenetic trees is done 10 times faster that before
• Creating pairwise comparison tables is done 10 times faster that before

Plug-ins

• Sequence reader - reads sequence aloud
• Recent items - show updated list of recently used data
• VNTI import - including import of VNTI archives

Example data

• Example data is included in the installation file - no need for download
• Large vector library included
• New RNA sequences

CLC Protein Workbench 3.0.3

The following has been updated:

• Better import of aln files
• Solved problem with annotation rendering when inserting long sequences
• Annotation labels are now appended when exporting into GenBank format
• BLAST binaries are updated to version 2.2.17 which fixes some issues on the Windows platform

CLC Protein Workbench 3.0.2

The following has been updated:

• BLAST databases are not indexed per default any more
• More information added to the BLAST output table
• Improvement of regular expression syntax in motif search
• A few help updates
• Better detection of memory on computers with more than 2 GB RAM
• Better license handling on Windows Vista
• Fixed error in alignment editing
• Improved program stability
• Improved ORF detection on negative strands of circular molecules
• Better file naming when importing raw sequence data

CLC Protein Workbench 3.0.1

The following has been updated:

• Better handling of PFAM databases
• Fixed error in conversion of old sequence data with lowercase characters
• Old data can now be converted through the help menu
• Fixed error when trying to save an element to non-selected location
• A few help updates
• Better license handling on Windows Vista
• Fixed error in alignment editing

CLC Protein Workbench 3.0

The following has been updated:

• Highlights
  • 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.
  • 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

• 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
• 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.

CLC Protein Workbench 2.2.4

The following has been updated:

• Import of VectorNTI database significantly improved

CLC Protein Workbench 2.2.3

The following has been updated:

• Better support for Windows Vista
• Improved import of Swiss-Prot files
• User can now select DNA or Protein sequence for Fasta import
• Minor BLAST changes

CLC Protein Workbench 2.2.2

The following has been updated:

• Improved import of GCG files
• Improved import of BLAST alias files
• Workbench starts correctly on AMD64 linux distributions
• Fixed error when upgrading preference settings
• Fixed error in motif search if the search string is more than 127 characters
• Better handling when searching very large BLAST databases
• Fixed focus problem preventing interaction with Side panel

CLC Protein Workbench 2.2.1

The following has been updated:

• The list of available BLAST database has been updated
• Now it is possible to use multi-volume blast databases
• Fixed error in the bugsubmission dialog when it was invoked by a workbench crash
• Fixed error in the preference panel when using empty BLAST url

CLC Protein Workbench 2.2

The following has been updated:

• Possible to install and use plug-ins
• Possible to develop your own plug-ins using our Software Developer Kit
• BLAST databases can now be defined by the user
• SignalP and TMHMM is now available through plug-ins
• Various bugfixes

CLC Protein Workbench 2.1

The following has been updated:

• Better secondary protein structure prediction
• Improved 3D viewing of molecules; among others including simultanious viewing of sequence structures in 2D and 3D
• Greatly enhanced web based BLAST. Longer sequences can be BLASTed, the graphical user interface is improved, and the subsequent handling of search results has been improved
• Enhanced BLAST on local databases. The graphical user interface is improved, and the subsequent handling of search results has been improved significantly
• You can now save HMM models generated in the Pattern Discovery function (searching for unknown patterns) - this reduces time for future pattern discovery searched significantly
• Advanced and interactive view of four different kinds of pairwise sequence comparisons:
  • Gaps
  • Differences
  • Identity
  • Jukes Cantor distances

These improvements and changes have been made in CLC Free Workbench and CLC Protein Workbench:

• Greatly improved data import: Manual work is reduced significantly when importing large amounts of data; e.g, when shifting from old software to CLC-software
• Much better handling of very large sequences: Much less memory use makes the application smoother to work with
• Significantly better data handling makes actions like deletion of files and working with many files at a time much faster
• Inclusion of pre-defined style sheets for the preference panel
• Greatly improved export of graphics
• Greatly improved printing
• Greatly improved file handling (faster etc.)
• Greatly improved save-function. Among others the option of creating new folders from the save dialog
• Tables are now searchable
• All output of analyses can now be shown in table

CLC Protein Workbench 2.0.3

The following has been updated:

• Swiss-Prot parser can now download and handle files from the UniProt (9.0) release (updated file format)
• Swiss-Prot parser again handles multi-entry Swiss-Prot files
• Fixed error dialog on exit of the workbench if an external file is deleted while kept open in another program

CLC Protein Workbench 2.0.2

The following has been updated:

• Fixed rare cases where doubleclicking annotations in an alignment resulted in a wrong selection
• Fixed dialog when stopping BLAST runs in the process area
• References to BLAST databases are updated due to changes on the NCBI server

CLC Protein Workbench 2.0.1

These improvements and changes have been implemented in CLC Protein Workbench

• BLAST: Expectation values with decimals now works for all locales
• Nexus parser fully functional
• Bootstrap values visible bug fixed
• Alignment gap-cost overflow management
• Cut/delete in navigator improved
• Even more user-friendly import-dialog
• Atom-count in sequence statistics bug fixed
• Bug fixed when downloading BLAST hit from graphical BLAST output viewer
• Attempting to drag more than 100 sequences no longer opens viewers
• Improved import of nucleotides from Vector NTI
• Import of oligos from Vector NTI

CLC Protein Workbench 2.0

These improvements and changes have been implemented in CLC Protein Workbench

• All icons have been updated in order to support a more modern and platform-independent look

Database searches and pattern discovery

• BLAST output can now be viewed in a table format, giving an easy overview of the data
• BLAST can now be performed on local databases
• You can now build local BLAST databases
• Motif searches can now be performed by using regular expressions
• Motif searches can now be performed by using ProSite patterns

Protein analyses

• The 3D viewer has been improved in several ways:
  • Better parsing of PDB data
  • Integration with the 2D sequence viewer
  • Implementation of tooltips on atoms
  • The BLAST of PDB data has been improved
• The Protein report has been improved significantly and now also includes
  • Signal peptide prediction
  • Secondary structure prediction
  • Transmembrane Helix prediction
  • PFAM search results

These improvements and changes have been made in CLC Free Workbench and CLC Protein Workbench

• An action can be started by dragging a sequence to an action in the toolbox
• The restriction site analysis tools have been improved, making them more interactive and easy to work with
• Two or more sequences can now be joined into one
• Two or more alignments can now be joined into one
• The history log has been improved, giving an even better overview of past work tasks performed on a given element (an alignment, a sequence etc.)
• In order to give a better overview of sequences, they are now wrapped to fit the screen as default when they are opened.
• A large number of tool tips have been added
• All analyses have now an initial pre-defined setting of parameters. These parameters can be re-applied by the user’s choice
• Position specific information (e.g. the conservation score on an alignment) on sequences and graphs is now available by pointing to or selecting a position.
• DNA Strider data and PIR data can now also be exported (earlier only import was available)
• Import/export of NEXUS data
• Import of sequences in Staden format

CLC Protein Workbench 1.5.2

In CLC Protein Workbench, this has been changed

• The Java 3D program extension is needed in order to view protein-molecules in 3D. Java 3D is however not installed as standard on Mac OS X 10.3.x. A warning is now given if this extension is not present on your computer.

These improvements and changes have been made to CLC Free Workbench and all other Workbenches

• The phylogenetic tree function has been improved: The number of replicates (the bootstrap value) is no longer fixed at 100. Any value can now be chosen.
• It is now possible to cancel the process when exporting views to graphics file formats such as .jpg, .pdf, and .svg etc.
• It is now possible to cancel “license upgrade” from within the program (Help menu)
• When sequences are opened, they are now zoomed to nucleotide level per default. The prior default setting was “fit to width”.

These errors and problems have been fixed in CLC Free Workbench and all other Workbenches

• Restriction site analysis: In some situations, updating from an older version of CLC Free Workbench to CLC Gene Workbench, CLC Combined Workbench, or CLC Free Workbench 2.5 or 2.5.1, resulted in the program freezing when selecting restriction enzymes. This problem has been fixed.
• Export of GenBank search parameters did not always work perfectly. This is now fixed.
• Running different types of CLC Workbenches right after each other could result in errors in some situations. This is now fixed.
• The user is now told if no hits were found in a database search - e.g. a GenBank search.
• Help-description in the programs: Users having an older version of JavaHelp installed than JavaHelp 2.0 did sometimes experience missing or in-optimal help-texts. This is now fixed.
• In a few situations, import of ABI files was not done correctly. This is now fixed.
• In some situations, resizing of the application changed the toolbar layout. This is now fixed.
• Naming a workspace with the same name as an existing workspace can now be done without problems.

CLC Protein Workbench 1.5

In addition to all the improvements in CLC Free Workbench 2.5, these features have been added and improved in CLC protein Workbench 1.5:

• Advanced and integrated 3D molecule viewer
• Import of mmCIF and PDB structure files
• Transmembrane helix prediction using TMHMM
• Motif search (search for known patterns)
• Pattern discovery (search for unknown patterns), based on advanced HMM models
• Batch processing, allowing analyses on multiple sequences at a time, performed as one work-step
• Antigenicity analyses
• Improved BLAST search: Tabular view of search hits, and option of integrated download of one or more of the sequences of your choice
• Improved UniProt search function, making it much easier to perform consecutive searches

CLC Protein Workbench 1.2

A number of improvements and new features have been added in CLC Protein Workbench 1.2:

All 12+ improvements to CLC Free Workbench, including the 10 times faster alignment, and greatly improved graphics printing and exporting options are included in CLC Protein Workbench 1.2. Click here to read about the improvements to CLC Free Workbench.

In addition, these improvements are made specifically for CLC Protein Workbench 1.2:

Protein sequence analyses:

• Web based prediction of signal peptides and their cleavage sites. This is done by SignalP 3.0. (read more on http://www.cbs.dtu.dk/services/SignalP/)
• The report Protein statistics now include the di-peptide composition of the protein(s).
• The annotations on a protein sequence are now retained when you make a reverse translation from protein to DNA. This makes it possible to see the protein-annotations on the resulting DNA sequence.
• The comparative protein statistics can now include as many sequence comparisons as you like, without squeezing the table texts on the screen and in the print-out.
• Translation from DNA to protein: You can now translate CDSs and ORFs only, instead of translating the whole DNA sequence.

Alignments:

• It is now possible to align two or more existing alignments
• It is now possible to add sequences to an existing alignment and make a new alignment without changing the original alignment. This is especially valuable if you have manually annotated and edited the original alignment, and therefore do not want to do this manual work once more.
• It is also possible to add sequences to an existing alignment and realign it in a process where the original alignment is changed/dissolved.
• It is now possible to make fixed-point alignments, meaning alignments where you define certain areas that are to be aligned with each other. This is especially valuable if you know that certain areas of a number of sequences contain a given annotation, and therefore wants to be 100% certain that these regions are aligned.
• It is now possible to re-align selected regions of an alignment.