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Serial Cloner Changelog

What's new in Serial Cloner 2.6.1

Apr 9, 2013
  • ADDED:
  • a preference to limit or not the width of Seq & Prot windows
  • CORRECTED:
  • Detection of overlapping Primers in PCR
  • Bug in "show info" toggle under Windows and Linux
  • Slow down under certain Windows install due to autosaving
  • Error in definition of PreScission site
  • Save/Save As problem is PCR window
  • Insertion point position when editing a protein sequence

New in Serial Cloner 2.6.0 (Mar 7, 2013)

  • [NEW] Estimates Isoelectric point of protein sequences (DNA and Protein Sequence Window)
  • [ADDED] An option in the Preferences to select pK value tables to use for pI estimation
  • [ADDED] An option in the Preferences to use the Codon code from Codon Usage tables as a Genetic code used for translation
  • [ADDED] An option in the Restriction Map window to only translate nucleotides that are in uppercase
  • [ADDED] A button/menu to choose particular sites to be displayed in Restriction maps.
  • [ADDED] Scan for peptide Features in Protein Sequences
  • [ADDED] Inherit Features when reverse-translating a DNA sequence
  • [ADDED] A rapid switch between a DNA and Protein Align window
  • [ADDED] Non formatted copy of Protein sequence (Copy MoreÉ Menu)
  • [ADDED] Inherit Features when copying/Pasting Protein sequences
  • [ADDED] Display Features in Protein Align (Local Align)
  • [ADDED] A toggle button to highlight differences in aligned proteins
  • [ADDED] A shortcut (S) to quickly show or mask Features (in the Features tab of Sequence Windows)
  • [ADDED] 'Anchor' and 'Core' domains of Primers are now recognized as Features in Sequence Windows
  • [ADDED] A button to quickly select a full linear insert in the 'Build a Construct' window
  • [ADDED]ÊAdded a shortcut to 'Copy Non Formatted' [COMMAND-SHIFT-K]
  • [ADDED] A menu entry to go to Serial Cloner Forum
  • [ADDED] A menu entry to go to Serial Cloner Youtube Channel (tutorial)
  • [UPDATED]ÊIt is now possible to fully resize Sequence windows
  • [UPDATED] Absent sites are indicated in italic in enzyme chooser windows (Graphic and Restriction Maps)
  • [UPDATED] Unique sites are indicated in bold in enzyme chooser windows (Graphic and Restriction Maps)
  • [UPDATED] Parsing of NCBI sequences (Web Access) to take in account changes in NCBI pages.
  • [UPDATED] Improved parsing of sequences containing 'X' in the nucleotide sequence
  • [UPDATED] Changed shortcut of 'Copy All Sequences To Multifasta' to [COMMAND-SHIFT-J] instead of [COMMAND-SHIFT-K]
  • [CORRECTED] A Windows-specific interface bug the the 'Import Codon Bias' window
  • [CORRECTED] A bug sometimes preventing proper copy of images (Graphic map, Virtual Cut, shRNA) in the clipboard (Windows specific)
  • [CORRECTED] A problem arising with uncommon RE names like R1.BceSIV in the particular enzyme" chooser of the Graphic Map.
  • [CORRECTED] A problem [Gateway Cloning] with Features indication when the destination vector was antisense (att2-att1 direction)
  • [CORRECTED] A bug in the selection of the most used AA when reverse translating
  • [CORRECTED] A problem with "Select All" in Sequence and Protein windows
  • [CORRECTED] A File type problem associated to Serial Cloner files (breaking compatibility with Sequencher import in particular)
  • [CORRECTED] Ligation : Sometimes unnecessarily produced degenerate DNA
  • [CORRECTED] Gateway : generated DNA but then when then saved as unknown type
  • [CORRECTED] PCR : if done on "unknown format" sequence, incorrectly generated "Protein" type.
  • [CORRECTED] A problem updating Feature when undoing a modification
  • [CORRECTED] When pasting a protein sequence in GenBank format (NCBI) a protein sequence window is now correctly created.
  • [CORRECTED] A problem with the NCBI BLAST server when using non-ASCII characters in Sequence names
  • [CORRECTED] A problem with Feature display after a scan when only one Feature was found
  • [CORRECTED] A rare problem of Feature display in the Construct Window
  • [CORRECTED] A refresh problem when using character size different from 12 pt in Graphic maps.
  • [CORRECTED] A bug in the Restriction map windows where the first line of amino acid translation was shifted in codon mode
  • [CORRECTED] A bug related preventing the use of previously selected enzymes in the Virtual Cutter Window

New in Serial Cloner 2.5.0 (Mar 7, 2012)

  • [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 reverse 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 Protein 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 sequence file in the Finder/File Explorer
  • [ADDED] See Features of aligned sequences.
  • [ADDED] See Features and coordinates of aligned sequences when clicking on them.
  • [ADDED] Align degenerate sequences
  • [ADDED] A preference to show the AA letter aligned with the middle of the codon (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 the 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 Map)
  • [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 list 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 parent Sequence Window
  • [ADDED] Click on a 'house' icon in Graphic Map Window or Restriction Map brings 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 name 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 images (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 recognized 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 (Find/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' command
  • [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 multiple RE hits
  • [CORRECTED] A bug affecting protruding end sequence in the construct window when 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.

New in Serial Cloner 2.1.0 (May 25, 2010)

  • [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 (available by clicking the circled i in the 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

New in Serial Cloner 2.0.0 (Sep 22, 2009)

  • [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 Features/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] A short manual describing Features handling has been added as a pdf file.
  • [ADDED] Scrolling in sequences and graphic map windows using mouse wheel.
  • [ADDED] User can modify the width of the Graphic Map window
  • [ADDED] The size of the selected fragment is now displayed in the Graphic Map
  • [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 by double-clicking on the name or 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 the 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.

New in Serial Cloner 1.3.0 (Apr 24, 2008)

  • Virtual Cutter Window. Predict number and size of fragments upon restriction and simulate gel migration
  • 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.
  • A silent restriction 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).
  • A consensus sequence can be extracted after a local alignment.
  • 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.
  • Peptides can be numerically selected in the �information� window.
  • The DNA sequence corresponding to the selected peptide can be �back� selected.
  • Point mutation can be added when preparing a shRNA construct.
  • ORF can be found and translated in both strands using the Sequence and Find... windows.
  • Alternative start codons can be selected for translation.
  • 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.