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

Marcos Oliveira de Carvalho operon at cbiot.ufrgs.br
Fri Jun 3 08:46:12 EDT 2005

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/)



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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