CLC RNA Workbench 4.4

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 RNA 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 RNA Workbench 4.2.0

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 (note that annotations with joined regions are 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 RNA Workbench 4.1

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)

CLC RNA Workbench 4.0.2

Updates

• Better performance of files with many annotations
• Fixed an error in RNA Structure Evaluation
• Fixed error and improved performance of Join Sequences tool
• Various bug fixes

CLC RNA Workbench 4.0.1

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 RNA Workbench 4.0

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)

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 RNA Workbench 3.1.2

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 RNA Workbench 3.1.1

The following has been updated:

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

CLC RNA Workbench 3.0.1

General performance improvements

• Improved performance when handling large data sets

• 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 RNA Workbench 3.1

• 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 RNA Workbench 3.0

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

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 RNA Workbench 2.1.2

The following has been updated:

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

CLC RNA Workbench 2.1.1

The following has been updated:

• Various bug-fixes
• 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 RNA Workbench 2.1

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 RNA Workbench 2.0.1

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
• Improvement of a few issues regarding visualization of RNA structures on alignments

CLC RNA Workbench 2.0

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
  • Better progress measurement during download, installation etc.
  • Automatic update check
  • Integrated plug-in registration: SignalP, TMHMM, MLST
• 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

RNA

• Partition function calculation included
  • Calculates the complete secondary structure partition function.
  • Calculates the probabilities of all possible base pairs and the probability that any single base is unpaired.
  • Creates a plot of base pair probabilities.
  • The pairing probabilities are distinguished by color codes in both the linear- and the secondary structure editors.
• Structure scanning
  • Scan larger sequences for the existence of local stable RNA structures.
  • Creates a plot of structure formation probability. Statistical significance of a local structure can be seen as spikes in the graph.
• Hypothesis testing
  • Testing hypotheses about an RNA structure using added structural constraints
  • Probability assigned to hypothesis using the partition function
• Import and export of RNA secondary structures in different formats (ct / col / rnaml / xml).

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
  • Creating phylogenetic trees is done 10 times faster that before
  • Creating pairwise comparison tables is done 10 times faster that before
• It is now possible to extract all sequences from a sequence list, an alignment or a contig (File->Extract Sequences)

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 RNA Workbench 1.0.3

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 RNA Workbench 1.0.2

The following has been updated:

• 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 RNA Workbench 1.0.1

The following has been updated:

• 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 RNA Workbench 1.0