Hi, the emboss.default file, which comes with the distribution, contains some example definitions for databases. But they don't work out of the box. In principle there are two ways for database access from emboss: You can either have the data on a local file system and index them with the emboss utilities (dbxflat, dbxfasta etc.) or you can configure emboss to access remote databases via http. There is a chapter about database configuration in the documentation http://emboss.sourceforge.net/docs/themes/Databases.html which explains in detail how to configure database access.
Hope this helps, David. [EMAIL PROTECTED] schrieb am 11/07/2006 19:16:06: > Dear Sir, > > The commands "entret", "seqret", and "whichdb" don't work on my intel > Mac. > > http://www.csc.fi/molbio/progs/emboss/doc/programs/html/entret.html > $entret tembl:hsfau > Reads and writes (returns) flatfile entries > Error: failed to open filename 'tembl' > Error: Unable to read sequence 'tembl:hsfau' > Died: entret terminated: Bad value for '-sequence' and no prompt > > http://www.csc.fi/molbio/progs/emboss/doc/programs/html/seqret.html > $seqret > Reads and writes (returns) sequences > Input sequence(s): tembl:hsfau > Error: failed to open filename 'tembl' > Error: Unable to read sequence 'tembl:hsfau' > > http://www.csc.fi/molbio/progs/emboss/doc/programs/html/whichdb.html > $whichdb -showall > Search all databases for an entry > ID or Accession number: hsfau1 > Output file [outfile.whichdb]: stdout > <Nothing were shown> > > [About my Mac] > Mac OS X 10.4.6 > Darwin 8.6.1 > MacBookPro1,1 > Intel Core Duo > > I am looking forward to hearing from you. > > Sincerely yours, > > Haruo Suzuki > > -------------------------------------- > Let's start Yahoo! Auction - Free Campaign Now! > http://pr.mail.yahoo.co.jp/auction/ > _______________________________________________ > EMBOSS mailing list > [email protected] > http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
