[DAS] Why the sequence uploads may be needed.

[Audrius Meskauskas]

Dear Lincoln

The system that we are creating (Sight,
https://sourceforge.net/projects/jsight/) does automatic analysis realising
the user-assembled tree-like forkflow. The input part of the system is well
developed (large selection of web robot generators), but the output is still
just written to the xml and html log files. In addition, Sight is written in
Java that causes a numerous problems for the Perl, C++ and Python
programmers who try to integrate it into their applications. To improve the
interaction with other programs, we decided to implement work of the Sight
application in a server mode. The user assembles the workflow, then starts
the Sight application. Application starts as a DAS server. Then the user can
call his/her other programs that can be configured to submit DAS requests to
the local host and get the responses. Sight DAS server could work as a
wrapper against some single program, but it can also be configured to
perform some specialised analysis (say search for BLAST hist, located up to
52 amino acids upstream of the second transmembrane helix (if the one
exists), predicted by TmPred. Sight application could run on the same
computer as the programs that connect it. It it is required to integrate
analysis programs that are only supported under different operating systems,
it can also run on some another nearby located computer.

We think, the most common type of request for Sight DAS server would be
request to get the sequence features for the submitted sequence. The most of
the protein feature finders (TmPred, Coil, BLAST, etc) work in this way.
Some mechanism must be provided to declare the submitted sequence as protein
or nucleic acid (DNA, RNA) sequence. The sequence must be uploaded using
POST. For me it seems that the most similar DAS standard is the 'features'
request. I am implementing in this way at the moment. However it is not a
good idea to mix the database accession numbers and the raw sequences. The
accession numbers are short, but the protein or dna fragment can also be sho
rt. I would suggest to have a separate standard for a sequence.

Sincerely yours
Audrius
Ulm university
Germany