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CLC RNA Workbench Changelog

What's new in CLC RNA Workbench 4.5 Build 45002

Jan 26, 2011
  • New features:
  • BLAST tools have been redesigned
  • New Blast Database manager for easy administration and management of local BLAST databases. Read more.
  • 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. 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.
  • Motif search available in Side Panel
  • Dynamic annotations will be added for motifs defined in the Side Panel (similar to restriction sites). Read more.
  • 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. 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.
  • 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.
  • Various bug-fixes

New in CLC RNA Workbench 4.4 (Jan 26, 2011)

  • 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).
  • 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

New in CLC RNA Workbench 4.3 Build 4302 (Jan 30, 2010)

  • 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 fast 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.

New in CLC RNA Workbench 4.2.0 (Aug 19, 2009)

  • 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

New in CLC RNA Workbench 4.0.2 (Mar 13, 2009)

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

New in CLC RNA Workbench 4.0.1 Build 4011 (Feb 27, 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

New in CLC RNA Workbench 4.0 Build 4003 (Feb 4, 2009)

  • Support for interaction with CLC Science Server;
  • New advanced filtering and layout of tables;
  • Performance of graphs and plots improved;
  • Local BLAST is upgraded to use NCBI BLAST version 2.2.19;
  • Easy access to results, data and analysis log from the process area;
  • New notification system

New in CLC RNA Workbench 3.1 (Sep 19, 2008)

  • Improved performance when handling large data sets
  • Annotation handling improved for large and heavily annotated genomes
  • Export of graphs in csv format
  • Various bug-fixes.

New in CLC RNA Workbench 3.0 (Jul 1, 2008)

  • 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
  • a large number of improvements to stability, UI and data handling.