November 29th, 2011New plug-ins and plug-in updates:
·
MLST module updated
· Possible to download MLST schemes from any web site compatible with mlstDBnet
· When a new allele is called because the sequencing reads are not long enough, this is reported in the isolate view rather than "New allele"
New and improved features:
· Multi-site Gateway Cloning. You can perform multi-site gateway cloning and in a few clicks create your expression clones with multiple fragments. The existing Gateway Cloning tool has been expanded so that you can easily recombine several fragments as well as continue using it for the standard Gateway Cloning.
·
Process tagged sequences
· A summary report is now available with an overview of the number of reads per bar code.
· You can search for barcodes (MIDs) on both strands, supporting new 454 protocol.
·
Find Binding Sites and Create Fragments improved
· If your template sequence contains ambiguity nucleotides (like N, Y etc), these will no longer count as mismatches when checking your primers. Note that the primer base of course need to be covered by the ambiguity symbol (e.g. a T would still be a mismatch if the template sequence has an R, which means either A or G).
· Fixed: When using multiple template sequences, the choices to open or annotate a fragment from the fragment table did not work properly. They always applied to the first sequence although the fragment was located on another sequence (as indicated in the table).
· Exporting fastq format no longer includes redundant name of the read in the quality score line. Now the name only appears once per read.
Bug fixes:
· 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.
· Fixed: Set-up experiment would crash when using many samples.
· Fixed: Calculation of consensus sequence in read mappings: Sometimes a majority of gaps would be ignored and a base erroneously introduced in the consensus sequence. It occurs when 1) there is no coverage in an initial segment of the reference sequence, and 2) a gap is encountered in the global read alignment. From that point onwards, gap counts are included in the consensus vote, but they are taken from the start of the mapping (where they are all 0), so they are out of sync with associated base counts. High gap counts would then kick in further downstream, possibly making the consensus a gap where it should not be. We recommend checking your mapping results manually if you rely on using the consensus sequence for further analysis.
· Fixed: importing adapters for trimming and barcodes for de-multiplexing did not work properly for CSV files and empty rows in Excel files were not allowed.
· Fixed: Motif search did not exclude regions with Ns when the option "Exclude matches in N-regions for simple motifs" was selected.
October 13th, 2011New and improved features:
· You can switch between compactness levels by pressing the Alt key while scrolling with your mouse or touchpad.
· Translation in the Side Panel of nucleotide sequences now includes options to translate "All forward" or "All reverse" reading frames.
· Conflict table view of read mappings: reference positions also reported in addition to the consensus sequence position.
· Alignments: it is now possible to copy all annotations from one sequence to other sequences in the alignment.
· Cloning editor: number of restriction cut sites and motifs are shown separately for the sequence currently displayed and for all sequences in the list.
· Restriction enzymes updated with latest REBASE version.
· 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.
Bug fixes:
· 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: Experiments tables can now be exported in Excel and csv formats
· Fixed: BLAST searches at NCBI always searched nr or nt, regardless of which database was specified. This has been a problem since the release of CLC Main Workbench 6.0
· Fixed: Pattern discovery wizard failed when the tool is run for the second time.
· Fixed: Certain annotation types were mapped to generic annotation types when exporting sequences in Genbank format.
July 14th, 2011Bug fixes:
· 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.
· Fixed: A problem with microarray experiments where large experiments could not be analyzed.
July 14th, 2011New and improved features:
· All history entries will from now on include the version number of the software
· Performance of Excel 2010 exporter improved in terms of speed and memory requirements
· When using a license server, the Workbench user can now specify a custom user name which can be checked in the license server configuration. This makes it possible to get more fine-grained control of the users of the license server.
· BLAST
· BLAST parameters have been changed so that number of threads is 1 per default (there is a bug in the BLAST code provided by NCBI which makes it fails on certain data sets when using multiple threads)
· The "Mask lower case" option has been removed
· Tool to download BLAST databases from NCBI within the Workbench
Bug fixes:
· Fixed: Alignment-based primer design failed for columns with many gaps
· Fixed: "Find Binding Sites and Create Fragments" did not find binding sites where the primer extended the 5' end of the template sequence
· Fixed: Import of certain special Genbank files failed
· Various minor bug fixes
July 14th, 2011New and improved features:
· 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.
· Fixed: Import of GO annotation files did not work
· Various minor bug fixes
July 14th, 2011Bug fixes:
· Fixed issue with synonymous overhang characters in cloning editor
· Graphics export now works with restriction sites shown
· Gene Ontology Annotations can now be imported
· 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· Cloning tool re-designed to make it easier and faster to perform restriction cloning
· Restriction sites used to select target vector and fragment.
· Sequences can now be displayed in circular mode in the cloning editor.
· Only one sequence displayed at a time (there is a list at the top of the view to switch between sequences).
· Option to clone several fragments and adjust overhangs and orientation in one dialog.
· New cloning tutorial available for a quick introduction.
· 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, contigs, BLAST results and alignments.
· Batching functionality available for selected tools.
· Multiplexing: Process tagged sequencing data
· It is now possible to import and use a file with bar codes and sample names. This makes it easier to process data with a high number of multiplexed samples.
· You can specify separate output folders for each sample, making it convenient to batch process the subsequent analyses.
· 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 (requires manual edit of database file).
· The default set of codon frequencies can be expanded (requires manual edit of table files).
· 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.
· Various bug-fixes
June 16th, 2010New 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
· Performance of ACE export improved, especially for long reference sequences or read mapping tables.
· 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.
· REBASE collection of enzymes updated to latest version
· BLAST: In the overview BLAST table, it is now possible to extract query sequences. Read more
· Process tagged sequences: it is now possible to input barcodes on a comma-separated list. 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
· Normalization of expression data: it is now possible to do "Reads per 1,000,000"-style normalization of count-based data. Read more
· New preference group called "Data" to hold information about adapter sequences and Gateway cloning primer additions. Read more
Bug-fixes:
· Print of folder content now takes settings in the Side Panel into account
· Process tagged sequences of paired data: it was not possible to specify one read without sequence (necessary for Illumina barcodes using paired data)
· Better memory handling in conflict table
· Find in Side Panel: space are now allowed
· Genbank import: sequence name (LOCUS) was truncated to 18 characters
February 5th, 2010Bug fixes:
· Fixed error concerning naming of dots in PCA plot
· Error in folder editor that prevented all elements to be shown is fixed.
· Documentation on trim using quality scores has been updated
· Fixed error preventing manual editing of contigs under special circumstances
· Various bug fixes
December 15th, 2009New features:
Expression analysis:
· Volcano plots: you can now choose the values to plot on the x-axis. Choose between "Difference" and "Fold change".
· Table view of bar plots shows the same intervals as are shown in the bar plot.
· Generic importer for expression array data in tabular format. Read more...
· Generic importer for expression experiment annotation data in tabular format.
· Gene Ontology (GO) files can now be used to annotate an expression experiment.
· Tag profiling: You are no longer allowed to annotate tag samples, only experiments
· Side panel of experiment table has been re-organized to provide better overview.
· Opening consensus sequence including gaps will also put Ns before the consensus sequence starts and after it ends
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.
· 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.
· Primer design now supports PCR fragments longer than 5000 bp.
· Extract Sequences moved from File manu 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 unsaved data now gets a * rather than make the tab name bold and italics.
October 9th, 2009· Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones.
· Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments.
· In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improved Find Binding Sites and Create Fragments tool, you can extract the PCR product from the list of fragments through a right-click menu.
· Check primer specificity. As part of the improved Find Binding Sites and Create Fragments tool, you can search with a primer pair in a list of potential target sequences and see an overview table of binding sites and mismatches as well as potential PCR fragments.
August 19th, 2009New features:
· Create new contig from selection
· 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.
Heat maps and clustering improved:
· You can now perform different clusterings on an experiment and save them all. In the Side Panel you can switch between the different clusterings to show the corresponding heat map.
· Terminology change in the clustering dialogs: "similarity measure" and "cluster distance metric" are replaced by "distance measure" and "cluster linkage", respectively.
Annotating samples or experiments for expression analysis:
· This is now possible even if the number of features doesn't match the number of annotations
· You can now decide which column in the annotation file to use for matching to the sample or experiment. Because of this extra option, you can no longer include an annotation file when setting up an experiment. You need to add the annotations afterwards
· Microarray import improved:Added support for import of more versions of native Illumina BeadChip and GEO expression files
· 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)
· Export of sequence data in fastq format
· Now possible to perform detailed manual editing of contigs with up to 100,000 reads
· Improved performance when zooming large contigs displaying a coverage graph
Bug fixes:
· Microarray import: Fixed a bug that prevented import of expression data with white spaces in column names.
· Problem when adding annotations to an Illumina array file
· Fixed problems importing expression annotation files
· Fixed tblastn numbering issue
· Fixed problem with graphics export of contigs
· 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· Corrections to the ACE export
· Better performance of files with many annotations
· Fixed an error in RNA Structure Evaluation
· Fixed error and improved performance of Join Sequences tool
· Fixed error in Find Binding Sites on Sequence: no longer distinguish between lower and upper case
February 27th, 2009· Find in the Side Panel did not support spaces when searching for annotations
· In the cloning editor under special circumstances, an error occurred when replacing a selection with fragment
· Sequence statistics codon count were not correct when using sequences
· Fixed error when deleting a selected read in a contig
· Fixed error in experiment table under certain sorting and filtering combinations
· Fixed error when exporting alignments in aln format
February 4th, 2009· Expression analysis including digital gene expression
· Support for both microarray- and sequencing-based (RNA-Seq) expression data
· Visualization: Interactive heat map, table and scatter plot views
· Transformation and normalization tools
· Quality control tools including principal component analysis, MA- and boxplots
· Experimental design tools for two- or multiple group comparisons
· T-tests and ANOVA analysis with support for paired/repeated measures
· Multiple testing corrected p-values (Bonferroni and/or FDR)
· Clustering algorithms: hierarchical clustering, k-means and Partitioning Around Medoids (PAM) with support for various distance and linkage measures.
· Ability to import NetAffx annotation arrays and adding annotation to experiments
· Tools for Gene Set Enrichment Analysis (GSEA) and for Hyper-Geometric based tests for overrepresented annotation categories (e.g. 'GO'stats or specific protein pathways).
· Ability to work with Expression Arrays and RNA-seq results at the same time, enabling comparison of results
· Assembly
· Right-clicking a graph (e.g. coverage) on a contig lets you export the data points to a csv file.
· Multiplexing - Process Tagged Sequences now has an option to filter away groups with few sequences. This is an advantage if you have very ambiguous barcode definitions where sequencing errors would lead to a lot of "false" groups. These groups can now be filtered because of their small size. (The option is called "Minimum number of sequences" and is found in the third step of the wizard.)
· Importing assemblies with more than one contig creates multi contig tables (ace and cas file import)
· 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
September 19th, 2008· Improved performance when handling large data sets
· Import and export
· Contigs can be exported in ACE format
· Export of graph data points in csv format
· Various high-throughput sequencing improvements
· Possibility to open consensus sequence with gaps. Right-click the label of the consensus sequence in the contig view and select: Open Copy of Sequence Including Gaps. The gaps will be represented by Ns in the new sequence.
· Dynamic consensus graph removed from contig view. Since contigs now have a "real" consensus sequence which is also updated to reflect changes in the reads, the dynamic consensus sequence which is switched on in the Side Panel has been removed.
· Annotations can be transferred from reference to consensus sequence in bulk. Right-click one of the annotations and choose "Copy to Consensus Sequence" or "Copy Annotations of Type xx to Consensus Sequence".
· 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.
· Fixed bugs related to contig editing.
· Various bug-fixes.
June 29th, 2008· The following has been updated: New name. Same style. A lot of new and even better features, 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, multiplexing: Sort sequencing reads based on their name to facilitate batch runs and sort sequences based on tag/barcode within the sequence, more reliable license system, and a large number of improvements to stability, UI and data handling.
April 15th, 2008· A few bugs resolved caused by the MLST plug-in
· BLAST of contigs no longer changes the contig name
· Fixed issue with tooltip rendering of quality values on reversed sequencing reads
· 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
· Improvement of a few issues regarding visualization of RNA structures on alignments
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
· Automatic license server detection
· Advanced license borrowing enables off-line use of workbench
· 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, MLST
· 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, contigs 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.
· Significantly faster algorithm now including multi processor technology - more than 4 times faster
· New action to reassemble contig
· Interactive mouse-adjustment of trimmed and excluded regions of sequence reads
· Refined conflict annotations now includes both existing and resolved conflicts
· Possibility to trim for multiple user defined vector sequences
· New action to reverse contig
· New right-click action to add sequences to an existing contig
· Sorting of contig reads (like alignments)
· By hand (mouse)
· By name
· By length
· By start position
· Individual scaling of trace data: mouse-grab the trace graph and drag up or down
· Possible to insert gaps in consensus sequence (Delete)
· Import of ACE files (e.g. contigs from Phrap)
· IUPAC codes included in the Contig table
· Editing sequence reads dynamically updates conflict annotations on consensus sequence (state: conflict or resolved)
· New right-click option on a consensus sequence selection: Transfer Selection to All Reads
· Trimming is performed twice as fast
· 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
· Improved action to Show Enzymes Cutting Inside/Outside Selection
· New layout
· Easier to understand
· Improved filtering of enzymes cutting inside or outside the selection
· Preview of enzymes to be added to the side panel
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
· Greatly improved wizard for in-silico cloning
· Detailed table view of all available insert sequences
· Interactive overhang "editor": simple mouse interaction easily adjust sequence ends emulating exonuclease activity or Klenow fill
· Graphically advanced compatibility aid and check of sequence ends
· Easily find enzymes with compatible ends
· Inserted fragments now include annotations with information about the parent sequence and the performed cloning steps
· Common cloning vectors now included in Example Data
· Naming of sequences in cloning editor now reflects the enzymes which have cut
· 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
· 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).
· 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) fa
· 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
August 23rd, 2007· 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. Fixed error in contig editing. 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.
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
April 25th, 2007· Better support for Windows Vista
· Improved import of Swiss-Prot files
· User can now select DNA or Protein sequence for Fasta import
· Fixed assembly problem when deleting reversed read
· Minor BLAST changes
March 19th, 2007The 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.
February 1st, 2007· The list of available BLAST database has been updated. Now it is possible to use multi-volume blast databases. Fixed error when opening a selection of reversed reads in the contig editor.
· Fixed error when deleting single stranded regions in the cloning editor.
· 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· Alignment based primer design
· Alignment based TaqMan probe design
· Improved assembly and trimming of DNA sequencing data
· BLAST on local databases
· Building of local BLAST databases
· Integration of 2D sequence viewer and 3D sequence viewer
· Motif search using regular expressions
· Motif search using ProSite patterns
· Joining multiple alignments and multiple sequences into one.
· Change of look/icons
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