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DNA Baser Changelog

What's new in DNA Baser 4.10.1.13

Jan 23, 2014
  • Major improvements:
  • The mutation detection module has been dramatically improved. The following modules have been added
  • - Single organism (Multiploid, Diploid) mutation detection
  • - Different organisms (Haploids, Multiploids, Diploids) mutation detection
  • Automatic homopolymers error correction added.
  • The new 'Chromatogram Preview' allows you to quickly asses the chromatograms as you work with them. Also shows statistics for the current selected file.
  • Mini-chromatogram (overview) in Chromatogram Preview panel.
  • Internal base caller - Blazing-fast proprietary algorithm that uses a sum of 7 different algorithms to compute the data accurately. Used to determine secondary peaks, uncalled peaks, and QV info.
  • Advanced SNP detection - Offers you the most accurate solutions on the market.
  • Automatically cut bad ends (NNNNNNNNNNNNNNs) in files that contain no quality scores (such FASTA).
  • The GUI workflow was also massively improved. The interface in now based on 'Tasks'
  • The automatic end trimming (cleaning low quality regions that the end of the sample) was massively extended/improved.
  • Added Mutations tab in Project Manager. The user can change here the parameters for mutation detection.
  • SNP: Secondary peak detection added
  • SNP: The user can jump to Next Mutation and to Previous Mutation with Shift+Click
  • SNP: Added 'Use internal base caller to calculate quality values' checkbox
  • SNP: Added 'Detect mutations' checkbox on interface
  • SNP: Added 'Mutation detection parameters' on interface
  • SNP: The program can recompute the base for 'N' peaks.
  • SNP: Allows user to enable/disable the internal base caller.
  • SNP: The user can choose to show or not Ns as mutations.
  • SNP: Use ambiguity code for mismatches only when the QVs are similar
  • Chromatogram Viewer: Show link between bases and chromatogram peaks
  • Chromatogram Viewer: The user can now click a base to select/highlight it
  • Chromatogram Viewer: New button added to show/hide A, C, G, T traces independently
  • Chromatogram Viewer: Copy entire chromatogram to clipboard
  • Chromatogram Viewer: The user can choose if the chromatogram will show 'base letter', 'QV', or 'base position' under each peak
  • 'Chromatogram Preview' panel can also show the CG and AT percent
  • New uninstaller is available.
  • New shortcut added. By pressing F9 key the user can perform the current selected action (assemble, batch assemble, convert to Fasta, etc)
  • Feature added in 'Settings' panel: let user always choose if the program starts in 'Assembly mode' OR 'Last used mode'
  • Export all samples at once as SCF.
  • New checkbox in Task Manager: 'Open Tasks panel when current task ends'. If enabled, every time the user closes a tool (batch processing, Assembly window, form manager, etc) the Tasks Manager will appear.
  • New pop-up menu on the main 'Start action' button allows quick access to predefined assembly settings.
  • Improvements:
  • Improved: Better scroll bar in Chromatogram Viewer
  • The Vectors window moved in the Project Manager for faster access
  • Better reports (log) when converting SFF to FASTA
  • Better base selection in Contig Assembly window. The user can start a selection (click and drag) even if the starting base was already selected.
  • SNPs are shown as IUPAC code
  • The Chromatogram Viewer can handle now invalid (too short (less than 10 bases)) chromatograms
  • Show selected base info
  • 'Use rainbow color', 'Keep cursor on center', 'Highlight low quality bases' options shown in Assembly window/Chromatogram editor and also in Assembly Grid menu
  • Better menus in Assembly window
  • The 'Batch file convertor' tool can now use the filename as comment
  • New 'Info Center'
  • The keyboard shortcuts have been fully redesigned
  • Added a button in the main toolbar for easy access to Project Manager.
  • When the contig assembly is done the cursor is automatically moved to the first ambiguous base in contig
  • When a base is clicked in Chromatogram Viewer the Assembly grid jumps also to that base (sync editing)
  • The user can easily see in which mode DNA Baser runs currently (batch, single contig, viewer, mutation detection, etc)
  • Better hints in Assembly window
  • For flexibility, 'Minimum overlap' can be set to a much lower value
  • The Project Manager now shows also 'Hidden' folders
  • Minor improvements:
  • Added 'TheScientist' link/info in the Info menu.
  • Mutations shown in Purple color in ContigGrid
  • SNP: New button 'Highlight mutations' added. It has effect on all open chromatograms and contigs.
  • Focus line (dotted line) inside the focused cell is not shown anymore.
  • Added 'Load sample' button in Sequence Viewer
  • In 'Assembly grid' the 'Editor' is shown when the user presses Enter key (or double click it)
  • Added menu for easy access to SFF Workbench external tool
  • New icon for 'External Tools' menu.
  • Fixed:
  • The program shows the same News more than once.
  • The selection color cannot be changed in Chromatogram Viewer
  • Fixed: A strange message was shown on screen when news were found online
  • Fixed: The updater didn't searched for updates once per day
  • Fixed: Project Manager did not remember its size after restart
  • Fixed: The toolbar in Project Manager form looks bad when the form is resized
  • Fixed: Problems with the size of the 'Settings' window
  • Fixed: Show gray area (trimmed regions) correctly (from the beginning of the chromatogram)
  • Fixed: The Assembly Grid did not resize correctly when lots of samples were loaded.
  • Fixed: The last active chroma remained active when user clicked a non-chroma row
  • Fixed: Assembly Grid window height
  • Fixed: The MasterStarter (DNA Baser Network edition) application was starting out of screen. Now it starts centered.
  • Fixed: User could select the empty rows in Assembly Grid
  • Fixed: The program was not showing the correct icon when user was clicking the tabs in Project Manager
  • Fixed: the cursor was not visible when the 'Base position' track bar was set to maximum
  • Fixed: Problems with some SCF samples that contain no QV info
  • Fixed: Chromatogram Viewer - Active chromatogram not marked as active (in reddish color) when user clicked a row in Grid.
  • Fixed: 'Save sample' was doing the same thing as 'Save sample as'
  • Fixed: Problems with 'Filename pattern' when the input file name has dots in it

New in DNA Baser 3.5.4.2 (Apr 29, 2013)

  • Major improvements:
  • The mutation detection module has been dramatically improved. The following modules have been added:
  • Single organism (Multiploid, Diploid) mutation detection
  • Different organisms (Haploids, Multiploids, Diploids) mutation detection
  • Automatic homopolymers error correction added.
  • The new 'Chromatogram Preview' allows you to quickly asses the chromatograms as you work with them. Also shows statistics for the current selected file.
  • Mini-chromatogram (overview) in Chromatogram Preview panel.
  • Internal base caller - Blazing-fast proprietary algorithm that uses a sum of 7 different algorithms to compute the data accurately. Used to determine secondary peaks, uncalled peaks, and QV info.
  • Advanced SNP detection - Offers you the most accurate solutions on the market.
  • Automatically cut bad ends (NNNNNNNNNNNNNNs) in files that contain no quality scores (such FASTA).
  • The GUI workflow was also massively improved. The interface in now based on 'Tasks' (see image below)
  • The automatic end trimming (cleaning low quality regions that the end of the sample) was massively extended/improved.
  • Added Mutations tab in Project Manager. The user can change here the parameters for mutation detection.
  • SNP: Secondary peak detection added
  • SNP: The user can jump to Next Mutation and to Previous Mutation with Shift+Click
  • SNP: Added 'Use internal base caller to calculate quality values' checkbox
  • SNP: Added 'Detect mutations' checkbox on interface
  • SNP: Added 'Mutation detection parameters' on interface
  • SNP: The program can recompute the base for 'N' peaks.
  • SNP: Allows user to enable/disable the internal base caller.
  • SNP: The user can choose to show or not Ns as mutations.
  • SNP: Use ambiguity code for mismatches only when the QVs are similar
  • Chromatogram Viewer: Show link between bases and chromatogram peaks
  • Chromatogram Viewer: The user can now click a base to select/highlight it
  • Chromatogram Viewer: New button added to show/hide A, C, G, T traces independently
  • Chromatogram Viewer: Copy entire chromatogram to clipboard
  • Chromatogram Viewer: The user can choose if the chromatogram will show 'base letter', 'QV', or 'base position' under each peak
  • 'Chromatogram Preview' panel can also show the CG and AT percent
  • New uninstaller is available.
  • New shortcut added. By pressing F9 key the user can perform the current selected action (assemble, batch assemble, convert to Fasta, etc)
  • Feature added in 'Settings' panel: let user always choose if the program starts in 'Assembly mode' OR 'Last used mode'
  • Export all samples at once as SCF.
  • New checkbox in Task Manager: 'Open Tasks panel when current task ends'. If enabled, every time the user closes a tool (batch processing, Assembly window, form manager, etc) the Tasks Manager will appear.
  • New pop-up menu on the main 'Start action' button allows quick access to predefined assembly settings.
  • Improvements:
  • Improved: Better scroll bar in Chromatogram Viewer
  • The Vectors window moved in the Project Manager for faster access
  • Better reports (log) when converting SFF to FASTA
  • Better base selection in Contig Assembly window. The user can start a selection (click and drag) even if the starting base was already selected.
  • SNPs are shown as IUPAC code
  • The Chromatogram Viewer can handle now invalid (too short (less than 10 bases)) chromatograms
  • Show selected base info
  • 'Use rainbow color', 'Keep cursor on center', 'Highlight low quality bases' options shown in Assembly window/Chromatogram editor and also in Assembly Grid menu
  • Better menus in Assembly window
  • The 'Batch file convertor' tool can now use the filename as comment
  • New 'Info Center'
  • The keyboard shortcuts have been fully redesigned
  • Added a button in the main toolbar for easy access to Project Manager.
  • When the contig assembly is done the cursor is automatically moved to the first ambiguous base in contig
  • When a base is clicked in Chromatogram Viewer the Assembly grid jumps also to that base (sync editing)
  • The user can easily see in which mode DNA Baser runs currently (batch, single contig, viewer, mutation detection, etc)
  • Better hints in Assembly window
  • For flexibility, 'Minimum overlap' can be set to a much lower value
  • The Project Manager now shows also 'Hidden' folders
  • Minor improvements:
  • Added 'TheScientist' link/info in the Info menu.
  • Mutations shown in Purple color in ContigGrid
  • SNP: New button 'Highlight mutations' added. It has effect on all open chromatograms and contigs.
  • Focus line (dotted line) inside the focused cell is not shown anymore.
  • Added 'Load sample' button in Sequence Viewer
  • In 'Assembly grid' the 'Editor' is shown when the user presses Enter key (or double click it)
  • Added menu for easy access to SFF Workbench external tool
  • New icon for 'External Tools' menu.
  • Fixed:
  • The program shows the same News more than once.
  • The selection color cannot be changed in Chromatogram Viewer
  • Fixed: A strange message was shown on screen when news were found online
  • Fixed: The updater didn't searched for updates once per day
  • Fixed: Project Manager did not remember its size after restart
  • Fixed: The toolbar in Project Manager form looks bad when the form is resized
  • Fixed: Problems with the size of the 'Settings' window
  • Fixed: Show gray area (trimmed regions) correctly (from the beginning of the chromatogram)
  • Fixed: The Assembly Grid did not resize correctly when lots of samples were loaded.
  • Fixed: The last active chroma remained active when user clicked a non-chroma row
  • Fixed: Assembly Grid window height
  • Fixed: The MasterStarter (DNA Baser Network edition) application was starting out of screen. Now it starts centered.
  • Fixed: User could select the empty rows in Assembly Grid
  • Fixed: The program was not showing the correct icon when user was clicking the tabs in Project Manager
  • Fixed: the cursor was not visible when the 'Base position' track bar was set to maximum
  • Fixed: Problems with some SCF samples that contain no QV info
  • Fixed: Chromatogram Viewer - Active chromatogram not marked as active (in reddish color) when user clicked a row in Grid.
  • Fixed: 'Save sample' was doing the same thing as 'Save sample as'
  • Fixed: Problems with 'Filename pattern' when the input file name has dots in it

New in DNA Baser 3.5.1 (Apr 29, 2013)

  • New: Show 'Search not found' message when the searched sequence was not found.
  • New: Put a bunch of imported sequences in a list (feature requested by lcrerar/masonlive.gmu.edu)
  • New: The program is now monolithic (you can copy only the EXE file on a USB stick and take it with you).
  • Fixed: Automatic updater.
  • Fixed: error if the user deletes a column and then it tries to make a selection while holding Shift.
  • Fixed: the base position trackbar.
  • Fixed: Assertion error on search. Happens when the user managed to put the cursor in the empty (no bases) area.
  • Improvement: Don't let the user put the selection in the empty (no bases) area.

New in DNA Baser 3.5 (Apr 29, 2013)

  • Improved: GUI is now supporting Windows 7 themes:
  • Improved: Batch mode: The program is now checking if it can create output folders
  • Improved: Better Unicode support.
  • Improved: Loading text samples (Fasta, Seq) requires less RAM now. No (pseudo) chromatogram is created for simple text samples (Fasta, Gbk, txt, Seq).
  • Improved: Log (Make log compatible with DNA Baser Console. Save all text in log to disk (save project) and restore it later)
  • Improved: Message: "Information about contig is shown only if the 'Auto save contig to disk' (located in 'Project Options' tab) is active."
  • Improved: If there are un-assembled multi-Fasta files show this message: "Samples belonging to multiFASTA/multiGBK files will not be moved to Unassembled folder"
  • Improved: The vertical scroll-bar in Contig Map appears now only when necessary.
  • Fixed: Minor: After batch assembly it jumps to Log but the right corner icon in not correctly shown (it still shows the icon of the Sample Explorer).
  • Fixed: Minor: At startup, the text in Tutorials panel appears with large font when the program starts for the first time.
  • Fixed: Batch assembly (by name pattern): The program cannot assemble two pairs of samples if they are located in different folders.
  • Fixed: Batch mode: when loaded from disk, each project correctly shows only its own log
  • Fixed: Cannot insert new base at the beginning of a sample if its beginning was already trimmed
  • Fixed: Caption bar updates (flickers) too fast in Batch mode
  • Fixed: Delete column doesn't work properly when more than one base is selected. It happens when the deletion takes place at the beginning of the first sample but before the second sample starts.
  • Fixed: Double clicking a sequence to view says 'SEQUENCE ASSEMBLY STARTED' (which of course is not true)
  • Fixed: Message: "Bad confidence score found instead of a good confidence score"
  • Fixed: Problems with 'search bases' function when the cursor was placed before/beyond the beginning/end of the sequence. Solution: Don't allow cursor to be placed outside sample's body.
  • Fixed: Some samples cannot be assembled if they are using U bases instead of T
  • Fixed: The number of selected bases is not updated after a 'delete base(s)' operation
  • Fixed: When loading scf files the message 'File version: 3.00' appears twice
  • Fixed: When the Contig Map is scrolled up/down, the top/bottom of the blue viewer window is not updated.

New in DNA Baser 3.0 (Apr 29, 2013)

  • New features (major):
  • Save the entire project to disk (samples, contig, user editing and corrections, etc). It can be done manually and/or automatically.
  • Edit existing projects (Add/delete samples to project)
  • Remember the edits that the user made in contig/input samples when the contig is recalculated.
  • MRU (Most Recent Used Files and Folders) - Quickly re-open a sample file/project that was used recently.
  • Batch by name pattern based on separator (thanks to Stephan)
  • Tutorial panel (with animated logo and sound on new announcement). When the program starts for the first time it starts in tutorial mode
  • New auto-updater tool
  • New features:
  • Automatically start DNA Baser when a project file is double clicked in Windows Explorer
  • Added separate popup menu when the user clicks on Assembly Grid header (it contains 'Delete current sample', 'Sample properties', 'Save sample as', etc)
  • Added 'Sample' menu in Contig Assembly window
  • Added 'Project' menu in Contig Assembly window
  • Added 'Delete column' function
  • Added 'Create new FASTA sample' tool
  • Added 'Save contig as RC' menu
  • Added 'Save contig' button in Assembly window
  • Added "View log" button in Assembly window.
  • Added several new menus in ‘View’ main menu
  • Added icons for all tabs in Project Manager (16x16 and also 32x32 pixels)
  • Added top logo in Project manager
  • Added 'Mark as trusted/untrusted' button in Assembly window
  • Added 'Ruler offset' feature (under 'Project' menu)
  • The user can start the assembly even if there is a single multiGbk/multiFasta file in Project Manager
  • The caption of Assembly window shows the selection size (how many bases were selected by user)
  • The user can now stop the single contig assembly and batch contig assembly process by pressing the Esc key
  • Let the user drag and drop files directly into DNA Baser's main window. This will not add the files to the job list but it will make the Project Manager to navigate to the folder that contains the dragged files.
  • Added 'Export alignment as text file' function which saves the entire alignment to disk as text file
  • The user can scroll the Assembly grid from Contig Map (by dragging the blue selection)
  • The user can change the active sample in the Assembly grid from Contig Map (by clicking a sample)
  • 'Rainbow' colors for assembly grid background - Helps you to quickly stop ambiguities, mismatches, errors
  • Clicking on sample's name (first column in Assembly grid) makes the cursor to jump at the beginning of that sample
  • Hovering the mouse over Assembly grid's first column will show not only the file name of the sample but also its comment
  • For multi-Fasta files the first column of the Assembly grid shows the name of that file followed by incrementing numbers (one for each multi-FASTA sub-component)
  • Improvements:
  • Improved: Better Network package.
  • Improved: Dramatic improvements related to memory requirements have been made. Now you can assemble very long samples (at least two times longer than before) without running out of memory.
  • Improved: DNA Baser can open very large multiFasta files now
  • Improved: Batch assembly FASTA/SEQ/GBK sample viewer
  • Improved: Drag and drop file directly into the main form will open the file
  • Improved: Fasta2MultiFasta converter updated to open all supported file types (scf, abi, gbk, etc)
  • Improved: MultiFasta2Fasta converter updated to open all supported file types (scf, abi, gbk, etc)
  • Improved: Sequence assembly speed was dramatically improved (up to 30% in some cases)
  • Improved: Added 'Do nothing' option in 'File operation for invalid/un-assembled files' in Project Manager
  • Improved 'Batch by subfolders' and 'Batch by filename pattern'
  • 'Sequence recognition' window was improved
  • Move the "Automatically switch to log" checkbox under the log.
  • Some menu re-arrangement
  • Speed improvement
  • Many other graphic user interface improvements (such as colors in grid and contig map, layout rearrangement, etc)
  • Added (partial) support for samples that contain lowercase bases.
  • The level of trust for current contig is now reported in Log
  • Totally rewritten selection tool. The selection follows the cursor as it jumps between rows.
  • GUI: Contig bases that will not be saved to disk (because vector removal) are stroked out
  • GUI: The layout of the Assembly window was improved. One of the improvements is the search box which is now bigger and detached
  • GUI: Less flicker during program start up
  • GUI: More descriptive text for main buttons
  • GUI: The tool tips pop-up faster now
  • GUI: Better log for Batch Sample Processing
  • GUI: Ambiguities are shown in a different shade of red (different than low confidence score bases)
  • GUI: For better visibility the current selected sample is now indicated with an arrow and its background is yellow.
  • GUI: The reference sample is shown in pink color also in Contig Map
  • Better support for ABI files
  • Faster Job List (it was slow when lots of samples were loaded into it)
  • Untrusted ends are shown in dark shades also in reference
  • The log now show the total number of invalid samples
  • The Home/End keys moves the cursor to the beginning/end of current sample instead of beginning/end of Assembly Grid
  • The window size and screen position for 'FASTA Viewer' is remembered next time when the program starts
  • In the Assembly window the tool-tip now shows two values for the position of the base: the position counting the gaps introduced by the assembly process and the position without these gaps
  • Automatically associate DNA Baser with project files.
  • Fixed:
  • Some settings related to colors used are now stored/remembered after restarting the application.
  • Other bugs fixed