ACEDB for sequence management?

Jonathan Epstein Jonathan_Epstein at nih.gov
Thu Jan 29 17:09:24 EST 1998


Greetings,

I have recently transferred from the NCBI to perform a scientific
technical
support function at the NICHD.

I'm currently performing needs analysis for a laboratory which is
involved in
zebrafish sequencing and analysis.  They estimate that they will
sequence
up to 3000 clones over a period of time.  Based upon availability, it
appears that we will use an SGI Indy system to manage the database;
other
target platforms could be considered if necessary.

Among the functions which the database/laboratory management system
should
perform:

* Lookup by clone identifier

* Lookup by keyword

* semi-automatic insertion of new sequence records based upon email
from sequencing lab

* Storage/linkage to two-dimensional image data derived from Adobe
Photoshop.  There will be an average of two images per clone, with an
estimated size of 400 by 400 pixels in 8 bit color.

* Automatic BLASTing of new sequences against the NR databases.

* Automatic detection of open reading frames, where possible.

* Comparison of new sequences with the laboratory database itself,
possibly
using BLAST.


For some clones, association of the original entry with a subsequent
full-length sequence obtained at a later date.

Clones may also in turn need be linked with radiation hybrid mapping
information managed/analyzed through a tool such as RHMAPPER.

Based upon what I have read and heard, it appears that ACEDB may be a
suitable candidate.  However, it is unclear to me whether the
computational
aspects of this system can be integrated into ACEDB, and if so, how this
integration can be achieved.  I would appreciate the feedback on this
question, as well as alternate recommendations for public domain and/or
commercial software solutions.

I am also interested in learning about the stability of WWW ACEDB tools
(webace?), as well as any third-party tools for performing retrieval
from
ACEDB via the WWW.

Thanks in advance,

- Jonathan




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