IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

ACEDB database for viruses

Mike Cherry cherry at stout.Stanford.EDU
Fri Oct 6 16:25:18 EST 1995

In article <msalminen-0610951433170001 at hivgenome.hjf.org>,
Mika Salminen <msalminen at hiv.hjf.org> wrote:
>We are thinking of porting a large collection of genbank formatted viral
>sequences into an ACEDB based database. We are concerned with trying to
>retain as much of the information of the fields in the genbank entries as
>possible, and specifically wonder if someone outhere has tools developed
>for this purpose already (filters I mean). 
>We would especially appreciate advice ofrom someone who might have done
>this with another virus, since that would propably be really helpful for
>the deign of the database model.
>Thanks in avance for your replies,
>Mika Salminen

I think you will find that any feature used in GenBank/EMBL is
available in ACEDB.  There are a variety of converters available.
Below is a short list as a starting point.


All of these converters might be specific to a particular database
project.  That is they will take what they want from GenBank and
discard the rest.

----- My converter -----

Anonymous ftp from weeds.mgh.harvard.edu look in the

There are a few others in that directory too.

----- A recently announced Perl script -----

I don't know how much people want something like this, but...

I've written a Genbank to .ace conversion script in perl.  It handles
the latest version of Genbank flat format files and outputs into ACEDB
version 4 type ?Sequence and ?Paper models.  (The models we use have been
slightly changed from the distribution - a copy is enclosed.)  Most of the
Genbank features are handled, and the user can set an option to generically
handle the features for which I did not write specific code.  The feature
handling routines are in a separate file, so it's easy to extend them.

The tar file is available at:

Enjoy.  Also, please send me your comments (or requests, even).

/s/     Martin Ferguson
        mferguso at klab.agsci.colostate.edu

P.S. If anyone knows of some perl libraries to handle asn.1 data, please
        let me know.

----- GenBank ASN.1 to ACE -----

we've written such a beast also, but for the binary representation (ASN.1) as
well as for text files. It is written in C, uses the NCBI toolkit (see
http://www.ncbi.nlm.nih.gov/), and is able to decode Entrez Data with the
help of an additional program. It can be found at


More information about the Acedb mailing list

Send comments to us at archive@iubioarchive.bio.net