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.
Darren 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). -- ********************************************************************** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ********************************************************************** EMBL webpages: http://tinyurl.com/6xdltl http://tinyurl.com/667jrp Email: h...@embl.fr Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France **********************************************************************
