Serial Cloner

2.6.1 07 Apr 2013

Analyze and manipulate DNA sequences.


Developer website: SerialBasics

Serial Cloner is a Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization.

Serial Cloner 2.6 handles Features/Annotations and allows to define, import and export, customized lists of Features. User can annotate any sequence portion or use the automatic scan to detect common features. Serial Cloner can read and write DNA Strider-compatible files and also import or export files in FASTA format, MacVector, VectorNTI, ApE and GenBank files with their features as well as pDRAW32 sequences. Genbank/EMBL files can also be read or imported from internet using the included web interface. The included Web interface also allows to submit BLAST request directly from Serial Cloner Sequence windows. Serial Cloner can open protein sequences, align and reverse-translate them using defined codon-biais tables. Version 2.6 can now estimate the isolectric point of proteins using various methods.

Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. All the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. All key functions are accessible through 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 feature, a fragment or show single, double or multiple cutter all in the same window. Text-based Sequence maps are also generated and also display Features. Serial Cloner handles Annotations and Features both in the sequence and in the Graphic Map and can automatically scan for sequence Features. Features can be added to protein sequences and inherited from DNA upon translation (done using chosen genetic code).

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 set-up a PCR-based amplification or prepare synthetic adaptors. shRNA constructions based on pre-defined scaffolds are also automated. 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. During all these sub-cloning steps, Features present in plasmids and insert will be properly inherited.

Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server and extract a consensus. Features of the aligned sequences are displayed. A virtual cutter, a web browser with instant import of NCBI/EMBL entries and a silent restriction map generator are also provided. Serial Cloner also allows to export GenBank files as well as Fasta-formatted text files. It is also possible to save (or copy in the clipboard) multiple sequences to submit a multi-alignement request to Clustal. It is also possible to copy sequences in a formatted or unformatted way in the clipboard.

What's New

Version 2.6.1:
  • [ADDED] a preference to limit or not the width of Seq & Prot windows
  • [CORRECTED] Detection of overlapping Primers in PCR
  • [CORRECTED] Bug in "show info" toggle under Windows and Linux
  • [CORRECTED] Slow down under certain Windows install due to autosaving
  • [CORRECTED] Error in definition of PreScission site
  • [CORRECTED] Save/Save As problem is PCR window
  • [CORRECTED] Insertion point position when editing a protein sequence


OS X 10.5 or later


Current Version (2.x)


Version Downloads
Education / Teaching Tools
07 Apr 2013
OS X / Intel 32