DNA sequence assembly
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molecular biology software
scf trace assembly

Release history

 

 

 

 

 

 

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.
  • Remember the edits that the user made in contig/input samples when the contig is recalculated.
  • Delete samples from project.
  • Add samples to project.
  • 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 window (with animated logo and sound on new announcement). When the program starts for the first time it starts in tutorial mode

New features:

  • "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
  • Two new menus were added in Contig Assembly window ('Sample' menu and 'Project' menu)
  • Automatically associate DNA Baser with project files.
  • Automatically start DNA Baser when a project file is double clicked in Windows Explorer

Details

 

 

 

What's new in version 2?

 

 

DNA Baser v2.9

  • New functionality: 'Chromatogram editor'
  • New functionality: 'Convert from ABI to SCF'
  • New functionality: 'Properties' menu added for chromatogram. You can get a detailed report about the current selected chromatogram.
  • New functionality: Ruler
  • New functionality: Edit bases anywhere in contig window. User can insert/delete/edit any single cell or column in picture window
  • New function: 'Auto open 'Settings' window tab if no contig was made'. With this, the user will be saved to open the 'Settings' window and then to navigate to the 'Assembler engine' tab manually.
  • Trimmed ends of the chromatogram (low confidence score bases) are marked in gray, in chromatogram viewer.
  • Auto scale peaks in chromatogram: peaks' height will auto adjust the panel's height
  • New options for primer detection: 'Keep primer' and 'Remove primer' (available in 'Primers' window)
  • New FASTA/SEQ editor
  • Brand new auto-updater.
  • Un-official support for Windows Vista
  • Trial period can be extended (free) at request
  • Users can drag-drop a file in the Directory Box. DNA Baser will switch to that folder.
  • Button to open contig after it was saved to disk
  • Redetect primers every time a base was edited in Contig
  • User is informed what to do when no contig was made.
  • Speed improvement while scrolling the contig/chromatograms

 

DNA Baser v2.7

  • It remembers the position of the splitter in Project Manager window
  • Accept sequences containing N as primers
  • Better handling of invalid ABI files
  • Memory requirements improved
  • Metadata and batch metadata integration (RNA Baser only).
  • Batch sequence processing (automatic end trimming, vector removal, metadata integration, conversion, etc).
  • Button to open Windows Explorer in contig's folder, after sequence assembly.
  • Remove vectors from single chromatograms.
  • SEQUENCE ANALYSIS - mark all bases with a confidence level (confidence score) below a specified threshold, in red.
  • Resizable chromatograms.
  • Full support for low quality end editing.
  • Better Windows Vista compatibility for users without Admin privileges (Guest users).
  • Gbk (GenBank) to Fasta converter tool was integrated in DNA Baser Sequence Assembler.
  • Clone library dereplicator tool was integrated in DNA Baser Sequence Assembler.
  • Fasta to MultiFasta converter tool was integrated in DNA Baser Sequence Assembler.
  • MultiFasta to Fasta converter tool was integrated in DNA Baser Sequence Assembler.
  • Double clicking a sample file (SCF/ABI/FASTA/SEQ) in Windows Explorer will open that file in DNA Baser
  • Allow only one instance of DNA Baser: If the user double clicks a sequence and DNA Baser instance is already open, the sequence will be loaded into that existing instance (instead of opening a new instance). You can change this behavior by placing/creating a file called 'OnlyOneInstance' into the 'DNA Baser\System' folder.
  • A new menu button called 'Request a feature' was added under the "Info" main menu. You can use this button to communicate with us, request new features or send feedback about our sequence assembler.

 

DNA Baser v2.0 to 2.2

  • Generate report when corrupted ABI files was detected
  • The Primers window was redesigned
  • Better way of associating file types in 'Settings' window
  • The user can now create/add its own cursor. We also provide a set of cursors in different colors.
  • It is now possible to load sequences that are in different directories
  • The number of mismatches is now shown in the Caption bar of the Assembly window
  • DNA Baser can now detect the correct type of a file. For example, it will detect if you try to open a SCF file accidentally renamed as ABI.
  • Recognize the primer sequences automatically, without pressing the 'primers' button. [by Kees Roest]
  • Batch sequence assembly based on file name pattern
  • Support for ambiguity code in contig (while editing the contig/Grid)
  • MMX optimizations for graphics
  • Copy chromatogram to clipboard (for pasting into Word documents)
  • A hint window appears when moving mouse over the grid to show the current base and confidence score
  • It can assemble two different file types at the same time (for example SCF and FASTA)
  • New functionality: 'Chromatogram editor'
  • New functionality: 'Convert from ABI to SCF'
  • New functionality: 'Properties' menu added for chromatogram. You can get a detailed report about the current selected chromatogram.
  • New functionality: Ruler
  • New functionality: Edit bases anywhere in the contig window. The user can insert/delete/edit any single cell or column in the contig window.
  • Trimmed ends of the chromatogram (low confidence score bases) are marked in gray, in chromatogram viewer.
  • Support for chromatogram files containing non-standard bases (non-capitals letters like a c g t).
  • New FASTA/SEQ editor.
  • Better compatibility while running under accounts with non-administrator privileges.
  • Partial support for multi contig added.
  • When BASER starts for the first time it should start in 'Samples' folder
  • If the user will try to open a FASTA or SEQ file that contains gaps BASER automatically delete those gaps.
  • Clicking in the Grid on a row should bring the corresponding chroma in view (auto scroll to that chroma panel)
  • New feature: 'Show batch button in 'Project manager''
  • New feature: 'Append prefix at the beginning of the saved file'
  • New feature: 'Center cursor on screen'
  • Added support for ambiguity code in Primers
  • Ambiguity code is now supported in the 'Reverse Complement tool' also

 

 


 DNA chromatogram assembly
contig assembly software
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