Release History

• Updated March 31, 2010 as v1.7.1
  • Added 'Pattern' regular expression module
  • Fixed Null Pointer Exception on startup due to deprecated code
• Updated January 17, 2006 as v1.6.0
  • Fixed launching conflict introduced with QuickTime 7.0.4
  • Digest: Using "REBase 601" enzyme list
  • Allow launching with Java 5 (JDK 1.5)
• Updated May 11, 2005 as v1.5.9
  • Pairwise: Added numbering to right side of each alignment line
  • Digest: Using "REBase 504" enzyme list
  • Digest: Layout enzymes in row order rather than column order
  • Digest: To remove redundant or irrelevant enzymes; "Unselect" then "Forget"
    You will want to trim the enzyme list to increase performance
  • Digest: To restore all forgotten enzymes; "Use REBASE..."
    Working on a way to restore only desired enzymes
  • NCBI Fetch: Now requesting 'tinyseq' which only returns the basic sequence information
  • NEW!: "Features" from NCBI fetched sequences -- display only
  • Digest: Finished 'Fragments' panel to actually write out the fragment sizes
  • ORF: Added Zoom In/Out, Fit to Width
  • Pattern: Added Zoom In/Out, Fit to Width
  • Digest/Graphic: Added Zoom In/Out, Fit to Width
  • Features: Added Zoom In/Out, Fit to Width
• Updated April 12, 2005 as v1.5.8
  • File Saving: Fixed bug where newly created sequences would not be saved
• Updated April 11, 2005 as v1.5.7
  • Fixed FASTA format and file saving bug
• Updated April 8, 2005 as v1.5.6
  • Requires Java 1.4.2, available in Mac OS X 10.3.3 or higher
  • ORF: Added 'Translate from beginning...' checkbox so that partially cloned ORFs will still be found.
  • Format: Conserve case of sequence from the editor
  • File Saving: Conserve case of sequence from the editor when writing sequence files
  • Publish: Add six frame translation
  • Publish: Change format string to add more options; earier to remember
  • Digest: Add three frame translation to sequence output
  • Pairwise: For local aligments print the range of the sequences
  • Pairwise: Conserve case of sequences in alignments
  • Bug: Fixed non-fatal, yet annoying, "Fatal SAX Error" message
  • Preferences: Added "Implicit Preferences" to most analyses.
• Updated March 01, 2005 as v1.5.3
  • Works best with Java 1.4.2, available in Mac OS X 10.3.3 or higher
  • Pasting in a sequence creates a proper sequence object which in turn update the analsyis panels
  • Removing all sequences leaves the editor in working state
  • Can now type into the editor, after 20 characters it will guess the sequence type and create a sequence object
  • Renamed "Edit" menu to "Modify", will use "Edit" correctly in the future
  • Fixed really stupid error in saving FASTA files. Thanks to Alexandros Poulopoulos
  • Digest: Removed automatic enzyme unselecting -- bad idea
  • Digest: Added "Fragments" panel
  • Pairwise: Moved "vs Sequence menu into the "Pairwise" panel
  • Pairwise: Added sequence numbering
  • Pairwise: Aligns with the selected portion sequence in the editor
  • Patterns: New, uses regular expressions, avaliable only with Java 1.4.2
  • Re-engineered the messaging between the editor and the panels
• Updated February 14, 2005 as v1.5
  • Works best with Java 1.4.2, available in Mac OS X 10.3.3 or higher
  • Multiple windows in order to group sequences or to compare sequences side by side. Let's start thinking about multiple sequence alignments
  • The application remains active after the last window is closed
  • Added missing 'Publish' legend text
  • Saving panel contents to a text/image file
  • "Save As" provides default filename, preselects the Desktop for saving
  • Isoelectric Point uses Merck Manual pKa values, instead of L. Stryer 'Intro. to Biochemistry'
  • Digest enzyme selection cascades. To select all unique four cutters: start with All enzymes selected, then select Four cutters, then select Unique cutters.
  • Fetching NCBI protein sequences with IUPACaa encoding fixed
  • New pairwise alignment engine, see web site for link
  • Reverse complementing creates a new, derived Sequence
  • Shuffling a sequences creates a new, derived Sequence
  • Removed MORGAN module, took too much RAM. If you really need this module, e-mail me
  • Added silly icons to analysis tabs
  • Create a uniformly distributed sequence, 'Random'
  • Create a weighted distributed sequence, 'Sampled'
  • First cut at a restriction map layout.
  • Better sorting of enzyme and cut sites in 'Digest' report panels
• Updated January 13, 2005 as v1.4.1
  • Printing for all text analysis panels
  • Window minimization via command-key
  • Command-N, Command-S, Command-P
• Updated January 6, 2005 as v1.4
  • Added 2-bit and 4-bit decoding of NCBI fetched entries
• Updated January 21, 2004 as v1.3.1
  • Fixed bug where removing the last sequence did not clear the sequence editor
• Updated January 2004 as v1.3
  • Conformed to Jaguar and Panther "Info.plist" setting for Java applications
  • Changed file chooser to use native Macintosh instead of Java
  • Implemented "Save" and "Save As..." menu items
• Updated January 2003 as v1.2
  • Added restriction digest panel based on DNA Strider outputs
  • Need to finish Digest panel by by writing a detailed map
• Updated November 2002 as v1.1
  • Moved frame menus to Macintosh menu bar
  • Add internal oligo prediciton to Primer3 panel
  • Removed "Quit" button at the bottom of the frame
• Released September 2002 as v1.0

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