July 14th, 2011· Fixed: A cache-related bug which would sometimes result in errors when running large jobs.
· Fixed: The UniProt search has been updated to reflect URL-changes at uniprot.org.
July 14th, 2011· Local BLAST is faster when blasting against small databases
· Bug fixes
· Fixed: Joined annotations did not get the right off set when inserting a sequence in the cloning editor
July 14th, 2011· Graphics export now works with restriction sites shown
· Improved support for systems with 512 MB of memory or less
· Blast: Fixed issue with BLAST database creation taking too long under certain circumstances
· Blast: Fixed issue concerning errors when input sequence names contained illegal characters
· Blast: Fixed issue with Extract And Open option being erroneously disabled
· Blast: Option to enter custom Entrez Query limits in Blast at NCBI re-introduced.
· Blast: Improved speed when using Blast results as input to wizards.
July 14th, 2011· BLAST tools have been redesigned
· New Blast Database manager for easy administration and management of local BLAST databases
· More user-friendly way of creating and accessing local BLAST databases
· Much more stable design of both BLAST at NCBI and Local BLAST when running large data sets
· The SNP Annotation using BLAST tool has been discontinued
· See migration notes for using your old databases here
· Improved layout of restriction site annotations
· Linear view: There is a new option for displaying labels as "Stacked" which means that the labels of overlapping cut sites can be discriminated
· Circular view: There is a "Radial" option that will place restriction sites (and annotations) as close to the sequence as possible with a radial layout
· Improved layout of general annotations
· Linear view: There is an option to separate restriction sites and annotations in separate layers
· Circular view: There is a "Radial" option that will place annotations (and restriction sites) as close to the sequence as possible with a radial layout
· Motif search available in Side Panel
· Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites)
· Use motif lists to add your own motifs to the Side Panel
· Annotation table now available for sequence lists, mappings, mapping tables, BLAST results and alignments
· Support for exporting tables as tab-delimited files
· Audit option: manual editing of sequences will be recorded with an annotation on the sequence (this has to be switched on in the Preferences dialog)
· The default database of restriction enzymes can be expanded
· The default set of codon frequencies can be expanded
· Improved option to export and import Side Panel settings
· Memory allocation: the default memory allocation for the Workbench changes from 75% to 50% of available physical memory with a maximum at 50 GB.
· Bug fixes
· The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules
July 14th, 2011· Improved memory management in general: lower memory footprint and shorter management overhead pause
· 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
· 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
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
December 15th, 2009New features:
Deployment:
· 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.
· Expression data importers are now described in technical details in a separate section.
· 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
Miscellaneous:
· 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.
· Better progress feedback on various dialogs
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.
August 19th, 2009New 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
March 13th, 2009· Better performance of files with many annotations
· Fixed error and improved performance of Join Sequences tool
February 27th, 2009· 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
February 4th, 2009· 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
October 7th, 2008· Fixed problems when scrolling very large sequences
· Fixed problem when importing very large GenBank files
September 19th, 2008· 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.
June 29th, 2008· The following has been updated: application now available for 64 bit Java VM, support for data handling for larger sequence lists, view larger sequence lists, sequence views with annotations are rendered much faster, alignments: possible to batch delete sequences, alignments: possible to toggle marked status of sequences, advanced algorithm for Maximum Likelihood inference of phylogeny, use an imported fasta file as motif list, more reliable license system, and a large number of improvements to stability, UI and data handling.
April 15th, 2008· BLAST of contigs no longer changes the contig name
· A few other minor bugs have been fixed.
December 19th, 2007· 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
December 7th, 2007· 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)
· 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.
· 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
· 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
· 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
· Sequence reader - reads sequence aloud
· Recent items - show updated list of recently used data
· VNTI import - including import of VNTI archives
· Example data is included in the installation file - no need for download
· Large vector library included
· New RNA sequences
October 8th, 2007· 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
July 24th, 2007· 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
February 1st, 2007· 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.
July 12th, 2006· All icons have been updated in order to support a more modern and platform-independent look
· 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
· Better parsing of PDB data
· Integration with the 2D sequence viewer
· Implementation of tooltips on atoms
· The BLAST of PDB data has been improved
· 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
March 21st, 2006· Advanced and integrated 3D molecular viewer
· Transmembrane helix prediction (TMHMM)
· Antigenicity analyses
· Motif search (known patterns)
· Pattern discovery (unknown patterns)
· Batch processing of multiple analyses in one work-step
· Improved BLAST search options
· Improved GenBank and UniProt searches
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