Off topic: vector map editing and DNA sequence alignment software

From: Florian Schmitzberger
Date: 27 September 2011 16:42

Dear All,

What type of software are people commonly using these days for vector/plasmid map editing, making/visualizing vector maps, and aligning (small to medium size) DNA sequencing data? Preferably, it should not be too expensive and be able to write text files, readable by other programs.

I am familiar with VectorNTI, which is great for vector visualization and editing; but I find it somewhat expensive. Sequencher seems good to quickly align DNA sequences (such as from DNA sequencing) with templates, but is not free. I have been using ApE for while for alignments, but aligning many sequences is more cumbersome than in Sequencher; I have not tested if Sequencher is good at visualizing and editing plasmid maps.

Ideally, I would like to have a single program for both purposes (vector editing and DNA sequence comparison). Does something like that exist? What are the alternatives to above programs?

Thank you in advance.

Florian

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Florian Schmitzberger, PhD

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From: Mahmudul Hasan

Hi Florian,
May be you can try the software from CLC bio. The full version can be
used as trial for four weeks and the free limited one forever! I think
you can do most of your things with the limited one. The link to
download the software is www.clcbio.com/index.php?id=532.

Regards,

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From: Luca Jovine

Hi Florian,

Have a look at Serial Cloner - it's free, runs on OS X, Linux and Windows, and is really quite powerful - including the ability to export single or multiple sequences to FASTA format text files (however, it can only align two sequences at the time I'm afraid):

http://serialbasics.free.fr/Serial_Cloner.html

HTH, Luca

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From: Sampson, Jared

Hi Florian - 

I've used Geneious for a few years now and been pleased with it.  Also a "freemium" business model: Basic version is free, and Pro version price depends on the term and type of license (student, academic/government, or commercial).  I find the Basic version suits my limited molecular biology needs pretty well. They also have occasional "Geneious Days" (today happens to be one!) when the Basic version can use all the features of the Pro version.

Available for Linux/Mac/Windows in both 32- and 64-bit.

http://www.geneious.com/

--

Jared Sampson

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From: Darren Hart

Hello folks,
A couple of years ago, we had a related discussion which I cut & paste below. I still use Vector NTI which is expensive and bloated, but works well. I've also had good experiences with Gentle which is free and open source.

Darren

Thanks for the 38 replies, both on and off the bboard. I have tested some of them and my favorites so far are ApE and Gentle which are free and quite good. But there may be others that are also good and I missed.

Summary:

Firstly, good advice from Warren DeLano:

1. Be wary of relying upon "free" tools not based on open-source code.
2. Be extremely wary of "free" tools which come with a license manager.
3. Instead favor "free" software tools which strictly meet the established definitions of:
  Open Source: <http://www.opensource.org/docs/osd>,
  Free Software:  <http://www.gnu.org/philosophy/free-sw.html>, or
  Public Domain: <http://en.wikipedia.org/wiki/Public_domain>
since it is *only* those tools that can be safely taken for granted over the long haul.

      But be prepared to pay good money for good software!

Secondly, if you are going to stop using VectorNTI, export valuable files in .gb format before the program locks. If this happens, contact Invitrogen and they (might) issue a short time extension as they did for me.

Recommended programs:

Geneious and CLCbio workbench are professional polished products competing with VectorNTI – but CLC free version is just a plasmid viewer really.

Sebastiano and others - much much "easier" than VectorNTI is ApE (http://www.biology.utah.edu/jorgensen/wayned/ape/), which is multi-platform and very easy to use for simple tasks.
I tried ApE and was really impressed, once I got past the very simple looking format. This would do most of the things required for designing vectors and works with .gb format files – Darren

Serial cloner (http://serialbasics.free.fr/Serial_Cloner.html) suggested by James Stroud. It works only with fasta or .xdna files – so is really a DNA editor and seems to have limited Protein analysis functions, even displaying translated ORFs above DNA sequence. But splicing DNA sequences together seems efficient.

Mark Brooks - recommended BioEdit:
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
It has an old fashioned & cluttered interface, but does do sequence editing, translation into proteins, ClustalW alignments and contig assemblies (a bit like ContigExpress in Vector NTI). It opens ABI files for sequencing data, to view the chromatograms. It uses the external programs such as clustalw alignments or cap3 to do the contig assemblies, and its licence doesn't expire!

For storing everything, I put my primers, plasmid sequences, insert sequences in a MySQL database, with an HTML front end I wrote:
http://plasmidb.sourceforge.net/
Plasmi::db also has a "homespun" feel to it, and only works with Firefox, for example (not other browsers). There is a primer designer page, for traditional cloning by restriction digestion etc.. I can't pretend it's in the same league as Vector NTI, though. The data is stored in a non-proprietary format; database tables which can be viewed with either the HTML pages, or MS Excel, for example.

Andy Gulick recommends the "Workbench" suite at the San Diego Supercomputer Center. It allows you to maintain a database of protein and DNA sequence, has many tools, and allows  you to create subprojects to help organize.
http://workbench.sdsc.edu

Yong-Fu Li suggested Lasergene, but not enthusiastically due to requirement to reformat files and not very good editing functions.

Roger Dodd - PlasmaDNA which seems pretty good for the basics http://research.med.helsinki.fi/plasmadna/ .

Christian Biertümpfel recommends another free tool: pDRAW32 ( http://www.acaclone.com/ ).
It runs natively under Windows and with the emulator wine on Linux.

Francis Reyes - Not sure if it's been mentioned, but I personally use EnzymeX (http://mekentosj.com/enzymex/) .Also recommends PDF library organizer Papers (http://mekentosj.com/papers/) to be exceptional.

Juan Sanchez Weatherby - GCK2 (GeneConstructionKit) and another GeneInspector. They where pretty amazing and with lots of features for plasmid design, keeping history, sharing, and lots more. I suppose they must have improved quite a lot over the years. I can't remember what the license was like (money wise) but I think you can download a free version (doesn't let you save or print things but shows what you can actually do with them). The link you need to find them is http://www.textco.com/products/index.html

Bryan Lepore – Lots can be done just with with [1] expasy tools and [2] sequence manipulation suite, which is entirely downloadable for local use.
http://www.bioinformatics.org/sms2/about.html (Darren says:  I agree SMS is very useful indeed and can be run via their website – no installation)

There is GENtle which has a whole slew of tools associated with it.  There are versions for several platforms. http://gentle.magnusmanske.de/ it is pretty similar to Vector NTI (and open source for the ambitious).

For Macs:

Jovine Luca - DNA Strider (1.4) runs just fine on both Tiger and Leopard. For more info, you can contact the author directly: christian.marck_at_cea. Fr

You could also try Christian Biertuempfel's suggestion of pDRAW32: if it works under Wine on Linux, it should work under Wine (or the commercial equivalent Codeweavers Crossover) on OS X as well.

Roger Dodd - PlasmaDNA which seems pretty good for the basics http://research.med.helsinki.fi/plasmadna/ . It works under Mac OS X and Windows... and probably Wine on Linux too.

Jann Sterxx - Geneouis also runs on OS X. From my experience (past two years), the program works just fine. You can download the trial at http://www.apple.com/downloads/macosx/math_science/index1.html (second page).

--
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Dr. Darren Hart,


For funded access to ESPRIT construct screening via EU FP7 PCUBE: http://tinyurl.com/ydnrwg4



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From: Juha Vahokoski

Dear CCP4Pers,

also j5 might be a good choice. I am not personally familiar with the software, so I would happy to hear any comments. It also seems to cope with modern cloning techniques like SLIC.

clicking away at http://j5.jbei.org/index.php/Main_Page

Regards,
Juha

--
"Genius may have its limitations, but stupidity is not thus handicapped."
-Elbert Hubbard
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Juha Vahokoski
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