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 <mark.x.bro...@gmail.com>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 <h...@embl.fr>:
> > 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
>

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