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Even Better Free Molecular Biology Software: Serial Cloner

Content brought to you by New England Biolabs

In 2007, I wrote a couple of articles on the best free software for molecular biologists on Mac and PC. One of the highlights of those lists was a fantastic cross-platform for in silico DNA cloning, sequence analysis and visualization, called Serial Cloner (move over VectorNTI!).

sc-screen-smallThe creator of Serial Cloner, Franck Perez, contacted me recently to tell me that he had just released an excellent new version of the  software and asked if I would relay this to our readers. Well, as a big fan of Serial Cloner I am only too happy to oblige.

If you do molecular biology and you haven’t tried our Serial Cloner, I’d urge you to give it a go. It is very intuitive and is packed with features; from basics like constructing importing sequences, constructing plasmid maps and restriction mapping, through more complex things like sequence alignment, Gateway cloning and siRNA design.

Among the many improvements Franck has made in this new version are:

  • Automatic scanning for features in imported sequences
  • Importing VectorNTI, Genbank, EMBL, ApE sequences with features
  • Generation of MultiFasta formated sequence for Clustal submission
  • Recovery of unsaved sequence in case of unexpected quit
  • Impoved Import of NCBI/EMBL sequences (Web Access)
  • Alignments via NCBI BLAST2seq

Check it out at http://serialbasics.free.fr/Serial_Cloner.html

18 Comments

  1. sameerbau on February 8, 2011 at 7:41 pm

    hey!

    I used the serial cloner’s latest version and found it really useful.even though our lab does not have frequent cloning work,i find the double stranded viewer..really handy while designing primers..

    I was thinking if you could recommend some good pathway designer
    software.You know it really takes a lot of time for somebody not well
    versed with GIMP/photoshop/illustrator/corel to make their pathway
    images or explain concepts using pictures for some publication or for
    teaching to students or for condensing matter from various papers..

    And also is there a place to download stock images for making such illustrations?

    Kindly help…or maybe write an article on the same!(don’t forget to care about windows users too)

    cheers
    sameer

  2. Franck Perez on May 27, 2010 at 7:25 pm

    Dear all,

    Just a quick message to announce you that I released version 2.1 of Serial Cloner.
    It is a much improved version so I strongly advice users to update. A non-users to give a try !
    It is still, and will always be, a freeware (although donations are welcome).

    Main improvements (among tens of changes) :

    – [NEW] Define user’s Feature Collection (DNA, Peptide)
    – [NEW] Import/Export Features collections
    – [NEW] Export Sequences in GenBank format (with Features)
    – [NEW] Directly send BLAST request to NCBI.
    – [NEW] Two Companion Software to import MacVector files and to Reset Serial Cloner
    – [ADDED] Search for a peptide sequence using the Find window.
    – [ADDED] Scan and Display Features in the Sequence Map window.
    – [ADDED] New “Copy Formatted (Full Seq + Features)”
    – [ADDED] An pop-up drawing to illustrate cloning using the Build a Construct 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] A pdf file describing Features definition and detection in version 2.1
    – [CORRECTED] Various bugs and interface glitches
    – [CORRECTED] Much improved Linux version (although still not officially supported)

    • Els Melis on September 25, 2017 at 2:04 pm

      Dear Franck,

      Anno 2017, is there a way to import files from CLC Workbench into Serial Cloner?

  3. Edgardo Rivera Delgado on May 13, 2010 at 1:47 pm

    I must agree. I downloaded this program a while ago and it’s been really helpful. I like the virtual restriction digest. I can visually compare my gel band sizes to the virtual band sizes and create my own customized ladder. You can do almost anything you can do in a commercial software. All of this for free. Thanks for sharing Serial Cloner!

  4. Franck Perez on May 13, 2010 at 12:47 pm

    Hi Cristian,

    yes, sorry. It is taking more time than expected because of so many other stuff to get going in the lab. The version is ready. I just need time to write a small documentation and to update my web site… Hopefully, soon !

  5. Cristian on April 12, 2010 at 8:00 pm

    Hi Franck,

    I just wanted to let you know that the Serial Cloner is a great Software, way better than the one which everyone used in the past and now is not freeware nowadays..I don’t even want to pronounce its name anymore…because some guys let you first use it and exactly when you need it mostly, they decide to trade it for lots of money. And then you are in such a bad position, that even if the lab doesn’t have enough money, you are forced to buy it because you think there is nothing out there, which can keep up with their bloody software…well, they should know that there is something out there and that is Serial Cloner. I hope only one thing: that this software will be freeware forever…One question: when are you going to launch the next version? The one with customized scanning? Thanks and keep up the great work,Cris

  6. Franck on February 28, 2010 at 9:39 pm

    Hi Sebastian,

    do not hesitate to contact me at using the email address indicated on my web site.
    Anyway, sorry to learn that you had a pb using Serial Cloner. Sometimes, the pref file gets corrupted. Please try to start the soft while pressing [CTRL] and [SHIFT]. Serial Cloner should ask you whether it may reset the prefs. Say ‘yes’.
    I hope it will solve your problem.
    Best,
    Franck.

  7. Sebastian on February 3, 2010 at 4:35 pm

    Hi Franck,
    thanks in advance for this nice piece of software.
    I am running Serial Cloner2.0 on WinXP and was about to create a customized DNA Ladder with the “virtual cutter” tool,(which worked fine so far) when it suddenly crashed(for the first time). The program is stil useable since, but each time i try to start the virtualcutter the same bug occurs.
    **error message**
    “An exception of class OutOfBoundsException was not handled. The application must shut down.”

    Which is a pity since i really did appreciate this feature.
    Re-installing SC2.0 didnt helped as well.

  8. matt on January 17, 2010 at 4:22 pm

    agree – as linux + open-source fan i would also love to see this under an open-source license – hoping some linux developers would jump in. Right now i am using chromas and pdraw for creating plasmid cards and sequence analysis. But as my main os of choice is kubuntu i would love to have a stable version on this system – tried it out but didn´t get it to work yet.

  9. MadGenius on November 30, 2009 at 8:17 pm

    Hi Franck,

    I agree with Liam – open up the code so that someone can make it work on Linux.

    @Matthew & Liam – I’m trying out CLC sequence viewer right now – runs on Java, and works quite well on Linux.
    (http://www.clcbio.com/index.php?id=28)

  10. Liam on November 30, 2009 at 9:38 am

    Hi Franck

    I to would appreciate a stable linux version. I know this is freeware, but perhaps you could consider opening up the code, some that a linux coder could implement a linux build.

    Thanks

  11. Oana on October 30, 2009 at 12:44 pm

    Good news, then, I’ll try the new version. I have used serial cloner on my mac for my gateway cloning and it was a great help: easy to figure out, quick, basic tools i need readily available. And it’s free. Even if I have a licenses for other programs, this is the first one I open. I am curious if they implemented recombination possibilities for the later generation gateway vectors.

  12. Franck on October 23, 2009 at 9:41 pm

    Hi Matthew,

    Well the truth is that I could never really debug the Linux version. I did not have the development framework running on Linux. I now have it so I will give a try. My scare is that each implementation of Linux is different. My test using Ubuntu were actually not that bad so I decided to let the Linux version of Serial Cloner be public (with some warning though on my web site) but it seems worst than I thought. What I know is that, so far, the web functions of Serial Cloner should be avoided at the moment – it may behave better in the next version.
    In conclusion, I can only promise that I will try to debug better the Linux version for the next release although my main focus, sorry, will still be Windows and MacOS versions. But if you are interested to beta test the next version whenever I will have progressed, please, drop me an email (serialcloner at serialbasics.com).
    best,
    Franck

  13. Matthew on October 23, 2009 at 7:22 pm

    Franck,

    If you are listening, can you help?

    I’d really like to run your program on linux (ubuntu), but I am getting many errors:

    OK, so I tried it on Ubuntu Jaunty 64-bit,
    Jaunty 32-bit, Hardy 32-bit, and on my netbook Karmic 32-bit. All of
    them a no-go. This program spits no errors other than the dialog “An exception of class FunctionNotFoundException was not handled. The application must be shut down. Exception Message: Could not load SCDynamicStoreCopyProxies from SystemConfiguration.framework” and
    when I try to debug it (using strace), all the program outputs is that
    it segfaults — which I think to myself, “no sh*t, sherlock”. From the cryptic text in the dialog,
    it appears that it is not properly handling the error thrown when a
    function *in its own binary* is not found. I arrive at this conclusion
    just based on the fact the function name starts with “SC”.

    Wine failed
    on all of them, too. I ran it in XP on a virtual machine, and I’m
    willing to bet wine is failing because they use what appears to be a
    very non-standard window system.

    Is it possible that you have a solution or should I, too, stick with PlasmaDNA?

    Thanks for any help,
    Matthew

  14. bala on October 10, 2009 at 4:04 pm

    I’ve used an older version of Serial cloner, glad to see that it has been updated. Will definitely give it a try, thanks Nick & Franck.

  15. Reef Koh on October 10, 2009 at 4:30 am

    I’m an undergraduate research student. Just downloaded the software. It’s great.

  16. Franck on October 9, 2009 at 5:27 pm

    @ Kurt
    That’s a pretty harsh comment. A nice review from Nick and then, with only one short comment, you cleanly destroy it ! Unless you are using the Linux version which is not officially maintained, I am really surprised by your comment. Being the developer of Serial Cloner, I can tell you that I always answer to email of people reporting bugs or asking for new functions, so please, do not hesitate to contact me.
    What I can just tell people is that me and my lab are the primary users of Serial Cloner and that I would not accept, like you, that my lab use an unstable soft, even if I were the developer. Serial Cloner has been downloaded several tens of thousands of time and is used as the main program by many labs of friends and colleagues.
    What I can only tell people is : try by yourself; I hope you will like it !
    Do not hesitate to contact me if you need help or which to see additional or better implemented functions,
    best,
    Franck

  17. Kurt on October 9, 2009 at 4:40 am

    It seems quit unstable, and crashes frequently. I’ll stick to PlasmaDNA, it’s not perfect, but it does the job

    https://www.plasmadna.net/

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