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. Since 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.

Version 2.5 now allows to open protein sequences, align protein sequences and reverse translate proteins using defined codon biais tables.


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. A Linux version is also distributed. 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 supported. 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.


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 import codon frequency tables from the internet using a Web interface. It also allows to generate sense and antisense sequences to be obtained after bi-sulfite conversion.  

Clone in a Few Clicks
Contact Serial Basics

Sequence Alignment

Sequence Map

Web Access

Virtual Cutter

  1. What's new in Serial Cloner 2.6

  2. (see the available contextual help window to get more details on new functions)

  3. 2.6.1

  4. - [ADDED] a preference to limit or not the width of Seq & Prot windows

  5. - [CORRECTED] Detection of overlapping Primers in PCR

  6. - [CORRECTED] Bug in "show info" toggle under Windows and Linux

  7. - [CORRECTED] Slow down under certain Windows install due to autosaving

  8. - [CORRECTED] Error in definition of PreScission site

  9. - [CORRECTED] Save/Save As problem is PCR window

  10. - [CORRECTED] Insertion point position when editing a protein sequence

  11. 2.6.0

  12. - [NEW] Estimates Isoelectric point of protein sequences (DNA and Protein Sequence Window)

  13. - [NEW] MacOSX version now distributed as a signed application (Mountain Lion Gatekeeper compatibility)

  14. - [ADDED] An option in the Preferences to select pK value tables to use for pI estimation

  15. - [ADDED] An option in the Preferences to use the Codon code from Codon Usage tables as a Genetic code used for translation

  16. - [ADDED] An option in the Restriction Map window to only translate nucleotides that are in uppercase

  17. - [ADDED] A button/menu to choose particular sites to be displayed in Restriction maps.

  18. - [ADDED] Scan for peptide Features in Protein Sequences

  19. - [ADDED] Inherit Features when reverse-translating a DNA sequence

  20. - [ADDED] A rapid switch between a DNA and Protein Align window

  21. - [ADDED] Non formatted copy of Protein sequence (Copy More… Menu)

  22. - [ADDED] Inherit Features when copying/Pasting Protein sequences

  23. - [ADDED] Display Features in Protein Align (Local Align)

  24. - [ADDED] A toggle button to highlight differences in aligned proteins

  25. - [ADDED] A shortcut (S) to quickly show or mask Features (in the Features tab of Sequence Windows)

  26. - [ADDED] 'Anchor' and 'Core' domains of Primers are now recognized as Features in Sequence Windows

  27. - [ADDED] A button to quickly select a full linear insert in the 'Build a Construct' window

  28. - [ADDED] Added a shortcut to 'Copy Non Formatted' [COMMAND-SHIFT-K]

  29. - [ADDED] A menu entry to go to Serial Cloner Forum

  30. - [ADDED] A menu entry to go to Serial Cloner Youtube Channel (tutorial)

  31. - [UPDATED] It is now possible to fully resize Sequence windows

  32. - [UPDATED] Absent sites are indicated in italic in enzyme chooser windows (Graphic and Restriction Maps)

  33. - [UPDATED] Unique sites are indicated in bold in enzyme chooser windows (Graphic and Restriction Maps)

  34. - [UPDATED] Parsing of NCBI sequences (Web Access) to take in account changes in NCBI pages.

  35. - [UPDATED] Improved parsing of sequences containing 'X' in the nucleotide sequence

  36. - [UPDATED] Changed shortcut of 'Copy All Sequences To Multifasta' to [COMMAND-SHIFT-J] instead of [COMMAND-SHIFT-K]

  37. - [CORRECTED] A Windows-specific interface bug the the 'Import Codon Bias' window

  38. - [CORRECTED] A bug sometimes preventing proper copy of images (Graphic map, Virtual Cut, shRNA) in the clipboard (Windows specific)

  39. - [CORRECTED] A problem arising with uncommon RE names like R1.BceSIV in the particular enzyme" chooser of the Graphic Map.

  40. - [CORRECTED] A problem [Gateway Cloning] with Features indication when the destination vector  was antisense (att2-att1 direction)

  41. - [CORRECTED] A bug in the selection of the most used AA when reverse translating

  42. - [CORRECTED] A problem with "Select All" in Sequence and Protein windows

  43. - [CORRECTED] A File type problem associated to Serial Cloner files (breaking compatibility with Sequencher  import in particular)

  44. - [CORRECTED] Ligation : Sometimes unnecessarily produced degenerate DNA

  45. - [CORRECTED] Gateway : generated DNA but then when then saved as unknown type

  46. - [CORRECTED] PCR : if done on "unknown format" sequence, incorrectly generated "Protein" type.

  47. - [CORRECTED] A problem updating Feature when undoing a modification

  48. - [CORRECTED] When pasting a protein sequence in GenBank format (NCBI) a protein sequence window is now correctly created.

  49. - [CORRECTED] A problem with the NCBI BLAST server when using non-ASCII characters in Sequence names

  50. - [CORRECTED] A problem with Feature display after a scan when only one Feature was found

  51. - [CORRECTED] A rare problem of Feature display in the Construct Window

  52. - [CORRECTED] A refresh problem when using character size different from 12 pt in Graphic maps.

  53. - [CORRECTED] A bug in the Restriction map windows where the first line of amino acid translation was shifted in codon mode

  54. - [CORRECTED] A bug related preventing the use of previously selected enzymes in the Virtual Cutter Window

updated March 2012

Multi-Format import

Scan for Features

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


Molecular Biology DNA cloning plasmid software vector restriction enzyme ligase electrophoresis vector bacteria antibiotics vectorNTI APE pDRAW32 Invitrogen Biolabs Sigma genious dnastar genbank clustal EMBL

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 early support

Serial Cloner is a Molecular Biology software.

It provides tools with an intuitive interface that assists you in DNA cloning, sequence analysis and visualization.

Serial Cloner is freeware

and is available for MacOSX, Windows and Linux