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 nucleotide or peptide sequence, 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. With version 2.1, Sequence Features are visible in the Sequence Map.

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. The Collection of Features to be scanned for can be defined and modified by the user, imported and exported.

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. Import from MacVector is also possible now.  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. It is also posible to send directly BLAST request at the NCBI and obtain the result  inside a Web interface

Clone in a Few Clicks

Sequence Alignment

Sequence Map

Web Access

Virtual Cutter

Addition/Correction in version 2.1

What's new in Serial Cloner 2.1 (see the available online help to get more details on new functions)

- [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

- [CORRECTED] Much improved Linux version (although still not officially supported)

A short manual describing Features handling has been updated and added as a pdf file.

Multi-Format import

Scan for Features

pDRAW32

ApE, Fasta

GenBank

Vector NTI

DNA Strider

Thanks to Michael Goodson, Philippe Benaroch, Helen Schreiner, Heiko Flammann, Cariappa Annaiah, Tatiana Nedvetskaya, Leopoldo Palma, Jolita Seckute, ATSbio, Benjamin Dickins, Juliette Azimzadeh, Paris Margaritis, Javier Irazoqui, Hideshi Yagi, Miles Pufall and Jing Liang for their generous support