[Bioclusters] requested summary (genbank)

bioclusters@bioinformatics.org bioclusters@bioinformatics.org
Tue, 22 Jun 2004 15:02:36 -0400

 >Hi, I am really sorry, but I have been deleting all the genbank posts.
 >I don't suppose you could summarise the mails in one final post to the
 >Else I can just check the archives.


Sure.  Here is a summary of all replies to my initial question:

Nick Brockner wrote:

> Hi All,
> I am brand new to this list (and bio clusters in general. . . ).  Just  
> wondering if anybody has any experience downloading and housing  
> GenBank locally.

http://www.bio-mirror.net/  Not that hard, just need disk space :)

> Any info related to he process used to get the database and store it  
> would be greatly appreciated.

See the link.

Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615


You might want to try MyGenBank.  Information is at

http://homepage.mac.com/iankorf/mygenbank.html  and code can be  
downloaded at

It uses MySQL and is fairly easy and lightweight.  We've been using it  
for a couple of years.  Good luck.



Hi Nick,

We are offering a Product/Service that creates and maintains a mirror of
EMBL-Genbank in a Postgres Database. The Installation also comes with a
WebGui and Java API.
Let me know if you want to know more.

Best Regards



Hi Nick,

We are using SRS with great success. It can also maintain dozens of  
other databases, integrates tools such as EMBOSS and BLAST, and  
supports Sun Grid Engine. It is *not* lightweight or easy to  
administer, though. The upside is that you are getting a heavyweight  
commercial product that is free for academia.
SRS is from Lion: http://www.lionbioscience.com . The reference  
implementation is at EBI: http://srs.ebi.ac.uk

I'll be happy to answer any other questions.


Ran Rubinstein
Center for Bioinformatics Infrastructure, Hebrew University, Jerusalem,  


I have a few shell scripts and C programs that can download GenBank and  
sort according to organism. I'll be happy to post them.

Kenneth Geisshirt, M.Sc., Ph.D.   --   http://kenneth.geisshirt.dk/



On Tue, 22 Jun 2004, Nick Brockner wrote:

> Hi All,
> Just wanted to thank everybody who replied with great info on genBank.
>  It was very helpful.
> Thanks again,
> ************************************
> Nick Brockner
> System Administrator, Biology Computing Facility
> Hamilton College
> nbrockne@hamilton.edu
> (315) 859-4137
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

Nick Brockner
System Administrator, Biology Computing Facility
Hamilton College