For alignments, sequence lists and other sequence views, the right-click options to Open Copy of Sequence and Open This Sequence have been merged to Open Sequence. If a copy should be created, use Save As with the new sequence, or drag it into a folder in the Navigation Area.
Errors related to managing Workspaces have been fixed.
Fixed an error when translating DNA to protein. When more than 10 sequences were produced, the resulting protein sequence included X instead of * as stop symbol. We advice customers to re-run any analyses with the translation tool when using more than 10 sequences as input.
Frequently used tools. This is automatically updated based on which tools are used most frequently.
Favorite tools: Right-clicking a tool in the Toolbox allows you to add a tool to your favorites list.
Quick launch of tools: Pressing Ctrl + Shift + T shows a dialog for easy typing and launching tools.
Relevant view settings are now copied when switching between different views of the same data. As an example: if you have specified a set of restriction enzymes to display in the circular view of a sequence and switch to the linear view, these enzymes will also be listed in the Side Panel here. Note that the Side Panel settings are only copied to the new view if they have been changed by the user in the old view.
Performance when sorting of large tables has been improved
Rename can now be done through right-click menu in Navigation Area.
Annotations on circular sequences:
When shown in linear view they have a cleaner appearance. Before, there was a line from beginning to end of the annotation, and this has now been removed.
When shown in circular view, it is no longer displayed as a joined annotation over the start point but as a continuous annotation.
Alignments: The performance of the algorithm for running multiple alignments has been improved and now runs on multiple cores.
Shortcut key for Translate to Protein has changed from Ctrl + Shift + T into Ctrl + Shift + P.
Fixed problem of not correctly formatting qualifiers in EMBL export.
Fixed a problem sorting sequence lists on modification date.
Various bug fixes.
CLC Sequence Viewer 6.7.1
Release date: 2012-09-05
Various bug fixes
CLC Sequence Viewer 6.7
Release date: 2012-08-09
It is possible to create sequence lists based on other sequence lists (not only single sequences)
Listing folder elements in the Navigation Area is faster
Translate to protein creates sequence lists when there are more than ten sequences
A new translation table added: Pterobranchia mitochondrial (see http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG24)
CLC Sequence Viewer 6.6.2
Release date: 2012-04-11
Aligned fasta import and export is now supported (see http://www.bioperl.org/wiki/FASTA_multiple_alignment_format). A consequence of this is that the standard fasta import of sequences will reject to import sequences that contain gaps, assuming they should be imported as alignments instead.
CLC Sequence Viewer 6.6.1
Release date: 2012-02-23
Translate to protein creates sequence lists as results when more than 10 sequences are produced. This greatly improves performance when translating large amounts of proteins
It is now possible to specify the number formatting in tables in the View Preferences.
Fixed: Downloading of protein sequences from NCBI fails.
Fixed: Opening external files (e.g. pdf files or Word documents) with spaces in the file name does not work on Windows.
CLC Sequence Viewer 6.5.4
Release date: 2011-11-29
New and improved features
Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.
Fixed: Annotations spanning the sequence from start to end did not display right when the sequence was wrapped. The annotation was only displayed on the first line.
CLC Sequence Viewer 6.5.3
Release date: 2011-10-12
New and improved features
Clean-up of the Workbench window so that it no longer holds information about which Workspace is active. This information is now displayed with check boxes in the Workspace menu.
Fixed: For circular molecules, the Find Open Reading Frames tool did not find reading frames on the negative strand. We recommend users to rerun any reading frame analyses on circular molecules.
Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format.
CLC Sequence Viewer 6.5.1
Release date: 2011-02-18
Improved support for Mac OS X systems with japanese language
Improved support for systems with 512 MB of memory or less
CLC Sequence Viewer 6.5
Release date: 2011-01-26
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. Read more.
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. Read more.
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.
Annotation table now available for sequence lists and alignments. Read more.
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). Read more.
The default database of restriction enzymes can be expanded (requires manual edit of database file). Read more.
Improved option to export and import Side Panel settings. Read more.
Memory allocation: the default memory allocation for the Workbench changes from 75% to 50% of available physical memory with a maximum at 50 GB.
The molecular weight calculation for the sequence statistics report is more accurate and is now reported for both single- and double-stranded molecules.
CLC Sequence Viewer 6.4
Release date: 2010-06-15
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.
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
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 Sequence Viewer 6.3
Release date: 2009-12-15
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 search, update notifications etc). Read more…
General import and export
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)
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).
CLC Sequence Viewer 6.2.0
Release date: 2009-08-18
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.
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)
Problem rendering scatter plots without lines
DNA strider files could loose name upon import
Rare misplacement of annotations when editing very large sequences
This update is recommended for all users.
CLC Sequence Viewer 6.1
Release date: 2009-06-02
June 2, 2009
Better feedback on processes: there is a tool tip showing details and start time.
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
Fixed error when parsing files from Clone Manager (cm5-files)
CLC Sequence Viewer 6.0.2
Release date: 2009-03-12
Better performance of files with many annotations
Fixed error and improved performance of Join Sequences tool
Various bug fixes
CLC Sequence Viewer 6.0.1
Release date: 2009-01-28
Find in the Side Panel did not support spaces when searching for annotations
Fixed error when exporting alignments in aln format
CLC Sequence Viewer 6.0
Release date: 2009-01-28
Improved user experience of processes
Non-modal feedback from processes:
When there is a message
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)
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
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.
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.