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I like BioEdit too. It is PC based, downloadable, and very easy to use. It allows copy-paste of a word or text file, and does alignment, translation, back translation, etc, and more. Fabulous program. I also use Lasergene which has the long standing DNA Star, Megalign, but you have to buy a license. It also requires changing format of files to text and saving with a specific suffix such as .seq which is inconvenient. You cannot copy and paste, and when you see a good alignment, you cannot copy and paste out either. Yong-Fu Li On Wed, Jan 28, 2009 at 7:43 AM, Mark Brooks <[log in to unmask]>wrote: > Hi Darren, > My favourite program for editing sequences (apart from > Vector NTI, which I suppose I'm going to have to delete soon), is > 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! BioEdit is quite > impressive, and sometimes I use it instead of Vector NTI, even > (honestly!). > > 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. > > I never really believed that Vector NTI was going to stay free (even > to universities etc.) for a long time, and I do think that they > deserve some money for their (excellent) product. I hope that they can > decide on a reasonable pricing scheme though, instead of vacillating > between "huge sums" and "nothing". They seem to be heading towards a > moderate price nowadays, at least. > > Mark > > 2009/1/28 Darren Hart <[log in to unmask]>: > > Hello, > > After several years of offering the molecular biology software VectorNTI > > free to the academic community (their "open access program") and building > > up a huge user base, Invitrogen have suddenly announced that they will no > > longer renew these free licences and the existing ones will be left to > > expire within the year. There are heavy renewal fees for anyone wishing > to > > continue use of this software. > > > > Can anyone recommend decent alternative PC compatible alternatives? Main > > uses are construct and primer design, plus simple quick alignments, > > sequence data analysis etc. The database structure for storing sequences > > was pretty useful also. > > > > Ideally free, otherwise reasonably priced. I've seen CLCbio and Geneious > > have products, both free and paid. Any experience? > > > > Thanks, > > Darren > > EMBL Grenoble > > > > ps anyone using VNTI might consider a backup of their work by exporting > > files to .gb format. I don't know if a locked up (expired) version > permits > > this and you will have no notice that it is about to expire. > > > > > > > > > > -- > Mark Brooks, > IBBMC, > UMR8619 - Bâtiment 430, > Université de Paris-Sud, > 91405 Orsay CEDEX. > Tel: 0169157968 > Fax: 0169853715 > Skype: markabrooks >