The current version of Serial Cloner is [2.1.0] - Sept 7th, 2009
It is still distributed as freeware (but I accept donations...).


Addition/Correction in Serial Cloner 2.1

- [NEW] Define user's Feature Collection
- [NEW] Handling of amino acid-based Features
- [NEW] Import external Features collections (Serial Cloner Format, Generic table format, ApE format)
- [NEW] Export Features Collections
- [NEW] Export Sequences in GenBank format (with Features)
- [NEW] Directly send BLAST request to NCBI.
- [NEW] Open degenerate Fasta sequences
- [NEW] A companion Software to Reset Serial Cloner Preferences in case of problem.
- [NEW] A companion Software to transform MacVector files to Genbank format compatible with Serial Cloner (from Davide Cittaro)
- [ADDED] Search for a peptide sequence using the Find window.
- [ADDED] Display Features in the Sequence Map window.
- [ADDED] Scan for Features directly in the Sequence Map window
- [ADDED] Create a Feature from a translated sequence
- [ADDED] New "Copy Formatted (Full Seq + Features)" menu to copy the Sequence as formatted in the Sequence Window (Copy More? menu)
- [ADDED] New "Copy as Genbank (Full Seq + Features)" menu (Copy More? menu)
- [ADDED] New Preference to set-up the minimum size of an ORF to be used when searching for all ORFs.
- [ADDED] New Preference to set-up the character size to be used in the Sequence Window
- [ADDED] New Preference to show or not the reverse strand by default in the Sequence Map
- [ADDED] New peptide Features added to Serial Cloner collection for automatic scan (e.g. tags like myc, HA, TEV sites, etc.)
- [ADDED] An pop-up drawing to illustrate cloning using the Build a Construct window
- [ADDED] Warns the user when using the Anti-Parallel, Reverse or Complement commands on only a portion of the sequence
- [UPDATED] Resizing the Sequence Window is now possible
- [UPDATED] Handling of Feature inheritance when sub-cloning (Build a Construct, Gateway)
- [UPDATED] List the ORF from the largest to smallest when searching for all ORFs
- [UPDATED] Better handling of scrolling when customizing display in the Sequence map window.
- [UPDATED] New Keystrokes can be used to select for Particular Enzymes in the Sequence Map (ARROWS, ENTER, ESC)
- [UPDATED] Improved parsing of Genbank sequences using the Web Access Window
- [UPDATED] Copying/Pasting now tries to keep Features
- [UPDATED] Better handling of scrolling of the RE list window
- [UPDATED] Better parsing of sequence when pasting a NCBI web page in a Sequence window.
- [UPDATED] Better handling of very short (few nucleotides) features.
- [UPDATED] Menu modification :  a new 'Features' menu has been added and Export functions are grouped together in the File menu
- [UPDATED] Menu modification :  a 'Copy More?' menu has been created to put together alternative Copy functions 
- [CORRECTED] Scrolling problems in the Sequence Window when selecting a large fragment.
- [CORRECTED] Detection of Att site when right at fragment extremities.
- [CORRECTED] Handling of type IIs enzymes
- [CORRECTED] Handling of Features when using the Anti-Parallel, Reverse or Complement commands
- [CORRECTED] Setting-up cohesive ends in the shRNA layout window
- [CORRECTED] A bug that made the HelpWindow appear "randomly"
- [CORRECTED] Various interface glitches
- [CORRECTED] Much improved Linux version (although still not officially supported)


Addition/Correction in Serial Cloner 2.0

- [NEW] Serial Cloner now handles Features/Annotations. Features can be added manually or by scanning (see bellow).  
- [NEW] A new panel in the Sequence Window to manage Feature/Annotations
- [NEW] A scan function (available both in the Sequence Window and in the Toolbar) to automatically detect Features. At the moment, it uses an internal database. The next version of Serial Cloner will allow to define user lists.
- [NEW] Automatic Scan available directly in the Graphic Map (available from the Toolbar or from the menu)
- [NEW] Add a Feature after selection of a segment in the Graphic map.
- [NEW] Selection of the feature sequence in the Sequence Window when double clicking in the feature name in the Graphic map.
- [NEW] Assemble and save a multi-Sequence Fasta-formated file containing all currently opened sequence (useful for multi-sequence alignment (e.g. CLUSTAL) submission)
- [NEW] Assemble and copy to the Clipboard a multi-Sequence Fasta-formated text containing all currently opened sequence (useful for multi-sequence alignment (e.g. CLUSTAL) submission)
- [NEW] Automatic recovery of unsaved sequences in (hopefully rare) case of crashing.
- [ADDED] Scrolling in sequences and graphic map windows using mouse wheel.
- [ADDED] User can modify the width of the Graphic Map window
- [ADDED] Drag and reposition the restriction sites and features names in the Graphic Map.
- [ADDED] Serial Cloner now tries to guess whether a degenerate sequence file is being opened.
- [ADDED] Import Vector NTI sequences with their features.
- [ADDED] Import ApE sequences with their features.
- [ADDED] Import Genbank Sequences (from a file) with their features.
- [ADDED] Several shortcut have been added for the major functions (Import, degenerate sequence, etc.)
- [ADDED] Use alt-click to reveal alternative commands now available in the Toolbar (New Degenerate Sequence, Import,  Interactive site usage).
- [ADDED] Automatic internet proxy detection using system settings (seems not to work if using a .pac file under MacOSX).
- [ADDED] MacOSX : a windows proxy (small black dot displayed in the red "close window" ball) is shown when the sequence has been modified and has not been saved.
- [ADDED] Sequence Names can be modified directly in the Sequence Window using a contextual menu available by CTRL-Clicking (or Right-clicking) on the Sequence name.
- [ADDED] Additional parameters can be set-up in the preference window (Internet Proxy management, Warning when importing non-Serial cloner files).
- [UPDATED] Extended contextual menu in the Graphic Map window
- [UPDATED] Correct Sequence Format indication displayed in the Sequence window when opening a sequence in a Genbank, EMBL, DDBJ, VNTI, pDRAW32 or ApE.
- [UPDATED] Import of NCBI sequences using the Web Access window (and the automatic parsing button) has been improved 
- [UPDATED] Alignment at NCBI using the BLAST 2 sequence software is re-established.
- [UPDATED] Improve import of sequence that nearly, but not fully, respect the layout of NCBI sequences (using the Web Access windows).
- [UPDATED] Change the interface of the window used to announce the availability of a new version.
- [CORRECTED] Handling of certain type IIs restriction enzymes like XXXXX,-a,-b or XXXXX,-a,+b.
- [CORRECTED] A crash occurring when changing CW/CCW without any selection done in Graphic Map.
- [CORRECTED] A bug in PCR occurring when amplifying very long sequences (more then 32 k)
- [CORRECTED] MacOSX : A bug in the behavior of the drawer window of the 'Manage Restriction Enzyme' window.
- [CORRECTED] A bug in the Fragment selection of the 'Build a construct' window.
- [CORRECTED] A rare bug in the Local Alignment that was deleting a portion of the aligned output
- [CORRECTED] A pop-up windows is no longer displayed indicating that the sequence was locked showed up when using the 'Save as.. ' command.
- [CORRECTED] The calculation of the % of aligned nucleotide in the Local Alignment Window has been corrected.
- [CORRECTED] A bug preventing Serial Cloner to import Fasta files containing accentuated characters in the header.
- [CORRECTED] MacOSX : An interface glitch in the 'Find' drawers of the Sequence Window
- [CORRECTED] WINDOWS : a problem with 'paste commands' in find window.
- [CORRECTED] A bug occurring when back selecting DNA from the translation field if the DNA was translated from the minus strand.
- [CORRECTED] A bug affecting degenerated restriction enzymes in the 'Build a Construct' Window.

Addition/Correction in version 1.3

- [New]: Virtual Cutter Window. Predict number and size of fragments upon restriction and simulate gel migration
- [New]: A small Web browser has been added.  Not only it allows to surf internet without leaving Serial Cloner but above all it detects automatically a NCBI or an EMBL entry and proposes to parse directly the entry in Serial Cloner format. The comments of the parsed sequence should contain key information.
- [New]: A silent map window has been added to see what site could be introduced in a sequence without changing the translation (not to be used on a full plasmid sequence as it can be quite long to generate).
- [Updated]: A consensus sequence can be extracted after a local alignment.
- [Updated]: Print character size can be set independently of screen character size. 8 pts are usually the best for printing and 12 for viewing on screen.
- [Updated] : Peptides can be numerically selected in the ?information? window.
- [Updated] : The DNA sequence corresponding to the selected peptide can be ?back? selected.
- [Updated] : Point mutation can be added when preparing a shRNA construct.
- [Addition] : ORF can be found and translated in both strands using the Sequence and Find... windows.
- [Addition]: Alternative start codons can be selected for translation.
- [Addition] : And I also added a function for the PCR experiments. When you select a sequence portion in a sequence window then, if there is a PCR window open a right clic in the sequence window will propose you to use the sequence as forward or reverse primer. It will then directly paste it (anti-paralleled for the reverse primer) in the PCR window.
- [Fixed] : several bugs fixed ( e.g. in Sequence Window, shRNA, Adaptor, Algnement), and interface fixes in particular under windows (toolbar glitch, behavior when reduced in the Taskbar, etc.). 


Addition/Correction in version 1.2

- [New]: Now complied as a 'Universal Binary'. 2-3x faster under Mac Intel.
- [New]: Added Local alignement algorithm with multi-frame translation in addition to remote NCBI Blast2Seq
- [New]: Toolbar added
- [New]: Re-designed Find window : now finds simultaneously all occurences of a sub-sequence, a restriction site or any ORF
- [New]: Now allows to manipulates degenerate DNA sequences (conatining other nucleotides than ACG or T)
- [New]: Homologous recombination option added in the Gateway cloning window (for yeast-type homologous recombination)
- [Fixed]: several bugs in Sequence Window, Sequence Map, and in Find.


Addition/Correction in version 1.1

- [New]: Printable Site Usage table (All site, Unique sites, Absent site)
- [New]: Genetic Code table window
- [New]: Standard Genetic Code table
- [added]: Multi-frame translation of Sequences aligned in BLAST 2 Sequences
- [added]: Opens pDRAW32 sequences
- [added] : [Windows] Possiblity to change character size of Sequence Windows (set in Pref Window)
- [added]: Change 'Copy' mode : now formated as 80 character-long lines.
- [added]: PCR fragments with protruding A for TA cloning (Pref option added)
- [Modified]: Manage RELibrary - Now can remove RELibrary from the list
- [Modified]: [Windows] Find and Info window now behave as a drawer window and are attached to the Sequence window.
- [Modified]: About window
- [Fixed]: several bugs in Sequence Window, Window List and in Extract Fragment.


Addition/Correction in version 1.02

- [addition]: Gateway(tm) cloning window for both LR and BP reactions [Gateway Cloning Window]
- [addition] : added a menu to the 'open matrix' button [PCR Window]. 
- [addition]: Improved Restriction Map display, now renamed "Sequence Map" : Translated DNA in Sequence Map can be presented as codons, numeric coordinates are now displayed [Sequence Map]
- [addition]: New preference option to choose how many recent file should be listed [Pref Window]
- [addition]: warning when non-ATGC nucleotides have been filtered out when pasting or opening a text sequence [Sequence Window]
- [addition]; Close all menu [File Menu]
- [addition]: add recently saved sequences now show-up in the recent files menu [File Menu]
- [correction]: display pb of sub sequence translation in Sequence Map [Sequence map]
- [correction]: Pb in scrolling  after pasting in seqwindow (under windows) [Sequence Window]
- [correction]: bug in the alignment of short sequences and updated display to take in account recent changes in NCBI BLAST2seq [Align two Sequence]
- [correction]: error when saving a new sequence using the CTRL-S shortcut [Sequence Window]


Addition/Correction in version 1.01

- New Short Harpin RNA building window added. This window allows to quickly build shRNA adaptors to be cloned in vectors like pSUPER or pSiRNA. A series of Layout (describing the cohesive ends, prefix, loop and suffix sequences) can be defined and stored.  The resulting oligonucleotide sequence can then be copied for ordering and the adaptor electronic sequence generated to be nserted in the target plasmid using the Build a construct window. The resulting shRNA structure can be copied as a picture in the clipboard. [Make shRNA Window]
- New Site Usage List table added. Available through an additional 'ShowSite usage Table' at the top of the Site usage window. This Table shows unique site in bold and absent sites in italic. It can be re-arranged (changing tha character size and the column number for Landscape or Portrait printing).  This table can be printed or copied in the Clipboard to be pasted elsewhere. [Site Usage Window]
- A print option has been added in the Restriction Map window. The character size and the page setup, as well as the number of nucleotides per line, can be adjusted before printing. [Restriction Map Window]
- Additional display parameters are now accessible in the restriction map window that can now be used as a 'Gene display' window as well. The reverse strand, coordinate 'dots' and restriction sites can be masked. Translation can be restricted to a portion of the sequence. [Restriction Map Window]
- Added the possibility to paste a full Genbank entry into the sequence field in a Sequence window. Simply copy the complete page obtained at the NCBI using your web browser and paste it in a new Sequence Window. Serial Cloner will extract the nucleotide sequence portion. The LOCUS name and ACCession number , and the CDS coordinate are pasted into the comment field. [Sequence Window]
- A New 'Copy as Fasta' (Commande-K on Mac / CTRL-K on Windows) function has been added in the Sequence Window. This format the copied sequence in the Clipboard in a Fasata format with a descriptive header followed by the sequence formated has 80 nucleotides per line. This is necessary when pasting a sequence in a web browser (for example to BLAST it) due to limitations in the size of text that can be pasted ub the text field of Web browsers. [Sequence Window]
-Added an option to erase Preference at when starting Serial Cloner. Useful when the Preference file got corrupted and prevent Serial Cloner from booting. To do so, oress CTRL+Shift when starting Serial Cloner. The preference then need to be set-up again.
- Corrected a display bug for blunt sites in the Enzyme Library window. [ Enzyme Library
- The Serial Cloner Icon has been updated. :-)

Addition/Correction in beta 15

- Added pop-up menus in the Construct window "Select DNA..." buttons to list currently opened Sequences and recently opened files. [Construct Window]
- Adaptors can be build "in memory", i.e. generating a new Sequence Window that contains all the relevant informations (sequence of the adaptor, cohesive ends, comments, name). This adaptor can be used directly in the Build a Construct Window,  using it new pop-up menus, without prior saving. [Adaptor Window]
- Lock button added to prevent unwanted modifications [Sequence Window]
- The Find routine now starts over from the begining of the sequence [Find Window]
- The Info window shows the ORF crossing or not the first stop encountered (new checkbox added to choose translation mode) [Info Window]
- The Enzyme list window is now complete. It memorises a list of recently used Restriction Enzyle libraries and allows to restrict the list to enzymes recognizing a target of a define length, or generating particular ends (blunt, cohesive...) and allows to add a new restriction enzyle (type II or IIs). Also allows to quickly find isoschizomeres or compatible ends. [Enzyme List Window]
-Align two sequences now works with short sequences. Added a checkbox to be selected when aligning short sequences. Note that, when using this option, Serial Cloner will choose the smaller sequence as 'Sequence 1'. [Align Window]
- Corrected a bug in Open Recent file Menu. [Menus]


Addition/Correction in beta 14

1- Sequences can now be locked to prevent unwanted modifications. Automatic locking of newly opened sequences is set in the preference window. [Sequence Window]
2- changes in the prefence window to incorparate the new lock option.  [Preference Window]
3- The enzyme list window is now complete. need to add an option to add new sites and save sub-lists. [Enzyme Library]

Addition / Correction since Version beta10-3

1- Correction of a bug preventing selection of the correct fragment when cut with Type IIs restriction enzymes [GrapMap] and [Build a construct]
2- Added a Restriction Library window displaying enzyme target sequences. Allows to quickly find izoschizomeres and compatible ends. This window is not complete in version 10-4 [Enzyme Library]

Addition / Correction since Version beta10-0

1- Help window available [Window Menu]
2- Sequence alignment through NCBI Blast2seq [Generate Menu]. An internet connection is thus necessary for this option.
3- Auto-check for update availability. Auto-check can be inactivated in the [Preference Window]
4- Network configuration (proxy) in the [Preference Window] (necessary for 2 and 3)
5- Site usage filtering ([Restriction Menu]): in the site usage window for <Sequence_1>, one can choose to display only sites that are absent or that cut at a particular frequency in <Sequence_2>. Particularly useful for example if you want to find a site that is unique in <Sequence_1> and absent in <Sequence_2>
6- In the Graphic Map ([Restriction Menu]), when selecting a particular site list, one can now choose to re-use the last set of selected site (from a previous Graphic Map).
7- Visualisation/modification of Linear Fragment cohesive ends ([Sequence Window]). you can for example use it to add a protruding A at the extremity of a PCR fragment or a protruding T to TA-cloning vectors.
8- A "Save Graphic Map As..." option has been added in the [File Menu]. Save as PICT under MacOSX or as bmp under Windows.
9- It is now possible to search in the antisense strand ([AS check box] in the [Find Window]). In the same window, when a type IIs site is found in the antisense strand, a backward arrow is shown. 
