All the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. Numerically select fragments, find restriction sites, ORF or  any motif, calculate Tm of selected fragments, %GC or dynamically determine the

translation your selection into peptide and calculate the MW using a compact interface.

Serial Cloner also lets you build text restriction map and quickly format it to add multi-frame translation or only show single cutters for example.

The graphic map of Serial Cloner is really Graphic as you can easily select and extract a fragment or show single, double or multiple cutter all in the same window. All the features are displayed on the map using user-modifiable colors; the features can be manually entered, imported from GenBank or automatically found after scanning by Serial Cloner.

Virtual PCR

Adaptor Synthesis

Ligate Fragments

Main Functions

Extract Fragments

Don’t clone alone

shRNA Set-Up

Fully Graphical Map

Sequence Window

Gateway(tm) cloning

Serial Cloner has been developed to provide a light molecular biology software to both Macintosh and Windows users. Serial Cloner reads and write DNA Strider-compatible files and import and export files in the universal FASTA format. Serial Cloner also import files saved in the Vector NTI, ApE, pDRAW32 and GenBank formats.  Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. Serial Cloner 2.0 now handles Annotations and Features both in the sequence and in the Graphic Map.

Overview

An intuitive Interface

Serial Cloner will assist you in setting-up new sub-cloning projects and in preparing the electronic versions of your constructs.

In addition to the classical restriction maps - both graphic and text-based - or site usage windows, you will be able to quickly extract a sub-sequence either in a selection or between restriction sites, to create a new

PCR-based fragment or synthetic adaptors. shRNA constructions based on pre-defined scaffolds are also automated. Finally, you can assemble fragments, obtained by PCR, adaptor/shRNA synthesis or simply by graphically selecting fragments between restriction sites. Just select, blunt if you need, and click the Ligate button. An additional interface allows easy Gateway(tm) cloning for both BP and LR reactions. Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server.  You will also find a Restriction Enzyme library management interface,  Additional tools, like a web browser for direct import of NCBI and EMBL entries, a virtual cutter to prepare restriction analysis or a silent restriction map generator to find how to introduce restriction sites without modifying the translated peptide are also provided.,

Clone in a Few Clicks

Sequence Alignment

Sequence Map

Web Access

Virtual Cutter

Addition/Correction in version 2.0

What's new in Serial Cloner 2.0 (see the available online help to get more details on new functions)

- [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] 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.

known issues/limitations :

- Lack of a complete manual (although the online help is pretty complete).

- User cannot define its own Feature database to be used when scanning. This will be for the next version.

Multi-Format import

Scan for Features

pDRAW32

ApE, Fasta

GenBank

Vector NTI

DNA Strider

Thanks to Michael Goodson, Philippe Benaroch, Helen Schreiner and Heiko Flammann for their generous support