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
