[BiO BB] A database system for in-house sequence collections

[Martin Gollery]

Hi Vered,

This depends on what the nature of the sequences are, and what data
you want to record. StackPack and Ensemble are both very good, as
Marcos has pointed out. If you want the system to keep track of
additional information about the clones, vectors, sequencing
conditions etc, then you might have a look at the MAGIC database
system from the Pratt group at University of Georgia. MAGIC keeps
track of all this information, which can be very useful when you have
to go back to it years later. Check it out at:
http://fungen.org/Laboratory/Bioinformatics.htm

Marty


On 6/3/05, Marcos Oliveira de Carvalho <operon at cbiot.ufrgs.br> wrote:
> 
> Hi Vered,
> 
> I have tested and used Sabia (http://www.sabia.lncc.br/), GenDb
> (http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/) and
> Manatee (http://manatee.sourceforge.net/) for microbial genome management
> and annotation (all are good tools, I recommend that you try each and see
> what fits better to your needs). For EST sequences I found StackPack
> (http://www.sanbi.ac.za/CODES/STACKPACK_REQUEST/) very useful. If you are
> looking systems for more complex genomes, you should try GMOD
> (http://www.gmod.org/) and ENSEMBL (http://www.ensembl.org/)
> 
> Cheers
> 
> Marcos
> 
> 
> 
> On Fri, 03 Jun 2005 05:03:00 -0300, Vered Caspi
> <veredcc at bgumail.bgu.ac.il> wrote:
> 
> > I am looking for a freely available software for storage (preferably in
> > MySQL), management and batch analysis of collections of sequences and
> > their annotations. The sequences are usually generated in-house by
> > various research groups.
> > We can currently allocate a single Linux server for this purpose.
> > Any advice will be highly welcome.
> >          Vered
> >
> > ===
> > Vered Caspi, Ph.D.
> > Bioinformatics Support Unit, Head
> > National Institute for Biotechnology in the Negev,
> > Building 39, room 214
> > Ben-Gurion University of the Negev
> > Beer-Sheva 84105, Israel
> > Email: veredcc at bgumail.bgu.ac.il
> > Tel: 08-6479034 054-7915969
> >
> >
> >
> >
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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS330
775-784-7042
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