The current version of Serial Cloner is [2.5.0] - January 2012 It is still distributed as freeware (but I accept donations...).

Addition/Correction in Serial Cloner 2.5 - [NEW] New protein menu - [NEW] Open protein sequence - [NEW] Protein align - [NEW] BLAST protein Sequence now in the protein menu. - [NEW] Reverse translation in the protein menu - [NEW] A preference option to choose the Codon usage table to be used for rever se translation - [NEW] 'Manage Codon Usage' window. - [NEW] 'Import Codon Usage' window to import tables directly from the web - [NEW] The name of the currently selected Codon Table is displayed in the Prote in Menu - [NEW] Choose genetic code - [NEW] Generate sense and antisense strand after C>>T bisulfite conversion - [NEW] Direct import of MacVector files (.nucl) - [NEW] Direct import of VectorNTI single and multisequence files (.ma4) - [NEW] Direct import of DNAStar EditSeq files (.seq) - [NEW] Preference setting to change Read out speed - [NEW] Transform a DNA sequence window into a degenerate DNA sequence and vice versa (menu and contextual menu) - [NEW] 'Copy Non Formatted' menu entry - [NEW] 'Remove duplicated Features' menu entry - [NEW] Menu entry (in the 'Sequence' Menu) to show the currently displayed sequ ence file in the Finder/File Explorer - [ADDED] See Features of aligned sequences. - [ADDED] See Features and coordinates of aligned sequences when clicking on the m. - [ADDED] Align degenerate sequences - [ADDED] A preference to show the AA letter aligned with the middle of the codo n (RE Map) - [ADDED] Incomplete ORF are now detected and shown in italic in the find window - [ADDED] It is now possible to find sequences, ORF and sites overlapping with t he origin of circular plasmid - [ADDED] A preference to modify Feature character size (Graphic Map) - [ADDED] A preference to modify RE name character size (Graphic Map) - [ADDED] A preference to choose to box or not RE-site/Features names (Graphic M ap) - [ADDED] A preference to choose or not to Box and color RE Names in Graphic map (Unique sites) - [ADDED] Parse (Import) Degenerate NCBI and EMBL GenBank format - [ADDED] Automatic recognition of pasted NCBI and EMBL degenerate sequences - [ADDED] Splitter in Sequence/Feature window. Allows to change size of the lis t Field in the Feature Tab - [ADDED] A button to show/hide unchecked RE sites in RE List window - [ADDED] Recover PCR windows after (hopefully rare) crashing - [ADDED] Rapid deletion of a Feature in the list (Seq Window) using ALT-DELETE or CTR-SHIFT-DELETE - [ADDED] ALT-Click on a Graphic Map Window or Restriction Map brings up the par ent Sequence Window - [ADDED] Click on a "house" icon in Graphic Map Window or Restriction Map bring s up the parent Sequence Window - [ADDED] Check all/uncheck all command in RE List - [ADDED] A preference to shift the toolbar of a few pixels vertically. - [UPDATED] Instant search in the Find window - [UPDATED] Colorize annotation when importing from non-serial cloner format - [UPDATED] Improved text contrasting in dark background (REsites, Graphic Map)

- [UPDATED] Improved parsing of Serial Cloner GenBank format - [UPDATED] Improve recognition of att site in the Gateway construction window - [UPDATED] Change character size of Graphic Map header depending on sequence na me size - [UPDATED] In the Find Window : Frame 0 is now labelled "3" - [UPDATED] Better conservation of Features when extracting a fragment - [UPDATED] Use the top-most opened sequence windows as default names in Align - [UPDATED] Avoid repetition of annotation detection when scanning - [UPDATED] Avoid duplicating Features when doing PCR, Ligation, etc... - [UPDATED] Better Toolbar appearance under Windows - [UPDATED] Switch to png format (instead of the deprecated pict) when saving im ages (Graphic map, Virtual Cut, suRNA) under MacOS. - [CORRECTED] Header of Graphic map now wrap properly - [CORRECTED] Graphic display of type IIs restriction sites. - [CORRECTED] Features with additional 5' or 3' sequences are now also recognize d in the anti-sense direction. - [CORRECTED] Display of very big DNA ladder (Virtual cut) - [CORRECTED] Sometimes an incomplete a nee in Align window - [CORRECTED] Problem of highlight when searching for sequence under windows (Fi nd/Sequence window) - [CORRECTED] A parsing problem when a Feature list was empty - [CORRECTED] A problem setting up character size in preferences for the RE map - [CORRECTED] Improved the behavior of the RE List window - [CORRECTED] Improved the behavior of choose site button in the Graphic map - [CORRECTED] A bug in coloring the text obtained after a "Copy as Formatted" co mmand - [CORRECTED] A display problem in RE List window (Blunt sites) - [CORRECTED] A display problem in RE List window (hidden sites) - [CORRECTED] A bug in the Find window sometime preventing the detection of mult iple RE hits - [CORRECTED] A bug affecting protruding end sequence in the construct window wh en using a full antiparallel liner insert - [CORRECTED] A bug that made SC crash if the first Feature category was empty. - [CORRECTED] A few cosmetic problems. 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 tabl e 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 probl em. - [NEW] A companion Software to transform MacVector files to Genbank format comp atible 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 a s 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 se arching 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 Seq uence Map - [ADDED] New peptide Features added to Serial Cloner collection for automatic s can (e.g. tags like myc, HA, TEV sites, etc.) - [ADDED] An pop-up drawing to illustrate cloning using the Build a Construct wi ndow - [ADDED] Warns the user when using the Anti-Parallel, Reverse or Complement com mands 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 ORF s - [UPDATED] Better handling of scrolling when customizing display in the Sequenc e map window. - [UPDATED] New Keystrokes can be used to select for Particular Enzymes in the S equence 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 Sequenc e 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 tog ether alternative Copy functions - [CORRECTED] Scrolling problems in the Sequence Window when selecting a large f ragment. - [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 Comp lement 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 support ed) Addition/Correction in Serial Cloner 2.0 - [NEW] Serial Cloner now handles Features/Annotations. Features can be added ma nually 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 Toolba r) 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 cli cking in the feature name in the Graphic map. - [NEW] Assemble and save a multi-Sequence Fasta-formated file containing all cu rrently opened sequence (useful for multi-sequence alignment (e.g. CLUSTAL) subm ission) - [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 cras hing. - [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 Gr aphic 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, dege nerate sequence, etc.) - [ADDED] Use alt-click to reveal alternative commands now available in the Tool bar (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 save d. - [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 automa tic parsing button) has been improved - [UPDATED] Alignment at NCBI using the BLAST 2 sequence software is re-establis hed. - [UPDATED] Improve import of sequence that nearly, but not fully, respect the l ayout 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 t hen 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 t he aligned output - [CORRECTED] A pop-up windows is no longer displayed indicating that the sequen ce was locked showed up when using the 'Save as.. ' command. - [CORRECTED] The calculation of the % of aligned nucleotide in the Local Alignm ent Window has been corrected. - [CORRECTED] A bug preventing Serial Cloner to import Fasta files containing ac centuated 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 Co nstruct' Window.

Addition/Correction in version 1.3 - [New]: Virtual Cutter Window. Predict number and size of fragments upon restri ction and simulate gel migration - [New]: A small Web browser has been added. Not only it allows to surf interne t 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 plasmi d 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 s ize. 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 ?bac k? selected. - [Updated] : Point mutation can be added when preparing a shRNA construct. - [Addition] : ORF can be found and translated in both strands using the Sequenc e 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 sel ect 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 forw ard or reverse primer. It will then directly paste it (anti-paralleled for the r everse primer) in the PCR window. - [Fixed] : several bugs fixed ( e.g. in Sequence Window, shRNA, Adaptor, Algnem ent), 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 additi on 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 nu cleotides than ACG or T) - [New]: Homologous recombination option added in the Gateway cloning window (fo r 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 (s et 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 a

re 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 C loning Window] - [addition] : added a menu to the 'open matrix' button [PCR Window]. - [addition]: Improved Restriction Map display, now renamed "Sequence Map" : Tra nslated 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 lis ted [Pref Window] - [addition]: warning when non-ATGC nucleotides have been filtered out when past ing 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) [Seq uence Window] - [correction]: bug in the alignment of short sequences and updated display to t ake in account recent changes in NCBI BLAST2seq [Align two Sequence] - [correction]: error when saving a new sequence using the CTRL-S shortcut [Sequ ence Window] Addition/Correction in version 1.01 - New Short Harpin RNA building window added. This window allows to quickly buil d shRNA adaptors to be cloned in vectors like pSUPER or pSiRNA. A series of Layo ut (describing the cohesive ends, prefix, loop and suffix sequences) can be defi ned and stored. The resulting oligonucleotide sequence can then be copied for o rdering and the adaptor electronic sequence generated to be nserted in the targe t 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 usa ge Table' at the top of the Site usage window. This Table shows unique site in b old and absent sites in italic. It can be re-arranged (changing tha character si ze 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 siz e and the page setup, as well as the number of nucleotides per line, can be adju sted 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, co ordinate 'dots' and restriction sites can be masked. Translation can be restrict ed 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 you r 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 C DS coordinate are pasted into the comment field. [Sequence Window] - A New 'Copy as Fasta' (Commande-K on Mac / CTRL-K on Windows) function has bee n 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 ca n 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 b e 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 cur rently 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 Wind ow, 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 Windo w] - 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 R estriction Enzyle libraries and allows to restrict the list to enzymes recognizi ng 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 q uickly find isoschizomeres or compatible ends. [Enzyme List Window] -Align two sequences now works with short sequences. Added a checkbox to be sele cted when aligning short sequences. Note that, when using this option, Serial Cl oner 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 lock ing of newly opened sequences is set in the preference window. [Sequence Window] 2- changes in the prefence window to incorparate the new lock option. [Preferen ce Window] 3- The enzyme list window is now complete. need to add an option to add new site s 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 wit h 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 connec tion is thus necessary for this option. 3- Auto-check for update availability. Auto-check can be inactivated in the [Pre ference 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 <Sequ ence_1>, one can choose to display only sites that are absent or that cut at a p articular 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 lis t, one can now choose to re-use the last set of selected site (from a previous G raphic 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 f ragment 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 antisens e strand, a backward arrow is shown.