MacResearch

Further to my own post, this might help some people out there.
I've been playing with seqret and come across a bit of a puzzle, that was solved with the help of Alan Bleasby at the EBI.

If you want to use seqret to search remote databases, e.g. the form

% seqret embl:ACC then the way to do it is have the following type of construct in emboss.default (which lives in /sw/share/EMBOSS/ in a vanilla fink install):


DB emblebi [
type: N
method: srswww
format: embl
release: "EBI"
dbalias: "embl"
url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
comment: "EMBL from the EBI"
]


Note that this constructs the correct query on the fly, and you don't have to muck around with building with %s and all that. Alan says that this format will make it into the next EMBOSS release in the emboss.default.template file. So, with the above, you'd use

% seqret emblebi:QUERY
.

However, the guys at WEHI seem to have screwed up because the following


DB embloz [
type: N
dbalias: embl
method: srswww
format: embl
url: "http://srs.wehi.edu.au/srs6bin/cgi-bin/wgetz"
]


returns a file that has 2 extra characters at the beginning, and seqret chokes on this. I'm going to ask them what's going on, if I can find an appropriate person.

The EMBOSS -debug option is really handy, by the way :)

Yah, and your help was much appreciated :)

Richard P. Grant http://www.rg-d.com/BioLOG/