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 yet powerful 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, MacVector, ApE, DNAstar, pDRAW32 and GenBank formats. Import from VectorNTI multi-file format is also possible now.  Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. Serial Cloner 2.5, handles Annotations and Features both in the sequence and in the Graphic Map and can automatically scan for sequence Features.

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.  Features are now visible when aligning locally. 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. Serial Cloner 2.5 now allows to manipulate protein sequences, do reverse-translation, and import codon frequency tables from the internet.

Clone in a Few Clicks

Sequence Alignment

Sequence Map

Web Access

Virtual Cutter

Addition/Correction in version 2.1

- [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] 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) (see provided example file)

- [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

- [ADDED] See Features in the alignment window.

- [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] 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 brings up the parent Sequence Window

- [ADDED] Check all/uncheck all command in RE List

- [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 wending PCR, Ligation, etc...

- [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] A rare problem 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.

Multi-Format import

Scan for Features

pDRAW32, ApE, Fasta, GenBank, MacVector, Vector NTI, DNA Strider, Text

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