[EMBOSS] Antwort: Genbank GI fetching?

[Niels Larsen]

Thanks David Bauer, for pulling me afloat. The dbxflat is
now grinding and I am making a small set of Perl accessors.

I saw a broken link at http://emboss.sourceforge.net, so
tried to see if there are more. The validator at W3C

http://validator.w3.org/checklink

gives a decent list in response to the EMBOSS link, with
the "recursive" option on.

Another little thing, but I might be wrong, is whether all
applications are listed in groups? for example, I go here
(from the home page),

http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/groups.html

and click about, hunting for seqret, but dont find (I wanted
to see which other related programs there is to seqret). The
"see also" tables give me that of course, but I didnt discover
that at first.

Finally question: I will build an accessor (in Perl) that
invokes seqret for pulling out a genbank sub-sequence, often
just a small piece, plus the features that overlap with this
piece. Can EMBOSS do this, or must I pull the whole entry,
parse and find the overlapping pieces in Perl?

I am working on these sites, which are only guaranteed to
work now and then,

http://biobase.com:8000/UTHCT
http://biobase.com:8000/RNAport
http://biobase.com:8000/RRNA

and I may use EMBOSS tools as part of a later query mechanism.
For now I will be using EMBOSS for filling in the non-matches
between the matches from a blast and other similarity reports,
for zoom-able alignments and better overview. And so far it is
going well with EMBOSS.

Niels L