Bringing the big news!

We have the great pleasure of presenting a brand new version of DNA Baser. We listened to you (to our customers) and implemented many of the features you have requested. One of these features is the "Save/load project". This allows the user to save the entire project to disk and re-load it later. All edits the user made will be restored exactly as left when the program was closed. Another important feature is "Add/Remove samples to/from project".

An upgrade path is available for existing customers. The download link for DNA Baser v3 can be found here.

What's new in version 3.5.1?

• New: Show 'Search not found' message when the searched sequence was not found.
• New: Put a bunch of imported sequences in a list (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.

What's new in version 3.5?

• 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 QV found instead of a good QV"
  
• 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.

What's new in version 3?

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 QV 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

  Building software together

DNA Baser is more user-friendly and more affordable than any other similar product on the market. It could not be this way without help from our customers and beta testers. By submitting feature requests, feedback and bug reports you help us to make a better product and to keep its price as low as possible. At the end you will directly benefit from it. Please don't hesitate email us or to chat (live) with us! Your opinion matters!

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