Georgios, Thanks for your reply.
I added your lines into the emboss.default. It works. But not for my own lines (I tried before subscribing this mailing list for help) like: DB embl [ type: N method: srswww format: embl release: "EBI" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?%s"; comment: "EMBL from the EBI" ] DB swissprot [ type: P method: srswww format: swiss release: "EBI" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";; comment: "SWISSPROT from the EBI" ] DB sw [ type: P method: srswww format: swiss release: "EBI" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";; dbalias: "SWISSPROT" comment: "SWISSPROT from the EBI" ] DB uniprot [ type: P method: srswww format: swiss release: "EBI" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz";; comment: "UNIPROT from the EBI" ] I'm confused how to use syntax. should I put 'srswww' or 'url' or 'entrez' after 'method'? and what kind of url should I put after 'url'? should I include or omit '%s'? It's difficult for a newbie like me to understand. On Sun, Aug 8, 2010 at 3:56 PM, Georgios Magklaras <[email protected]> wrote: > On 08/08/2010 08:02 PM, Hanquan Liang wrote: >> >> ... I know that >> I can download and make a local one, but that will take up a lot of >> space while just a small part of the entries are needed. >> > Depends on your data set. But I agree, if you do not need all of them, you > should not have to get them down. However, note, that remote access method > might not work properly sometimes and depending on the results of your query > (10-1000 sequences) it is a slower method to get things down. If you require > only some subsets of public databases, we can help you to create local > filtered sets. > >> In 'emboss.default' I tried to add databases, but the user document of >> EMBOSS is so out-of-date that I cannot follow it. > > It is indeed. Note, however, that the EMBOSS team is working on releasing > up-to-date documentation. > >> After several hours >> of searching and testing, I gave up and decided to come here for help. >> How do you guys use EMBOSS to access online public database? Can any >> one show me some of the lines in your 'emboss.default'? >> > The best method is to use a well working public SRS server. EBI has one. To > do that: > 1)Modify your emboss.default file to contain an entry like the following: > > DB special [ > type: N > format: genbank > method: entrez > fields: "id acc gi sv des org key" > url: "http://www.ncbi.nlm.nih.gov/sites/gquery"; > ] > > 2)Save the emboss.default and make sure you have your Internet connection > up. > > 3)Test your 'special' set with a query from the command line: > seqret special-des:H1N1 > > This should do the trick. > > -- > -- > George Magklaras > Senior Systems Engineer/IT Manager > Biotek Center, University of Oslo > EMBnet TMPC Chair > > http://folk.uio.no/georgios > > Tel: +47 22840535 > > > > _______________________________________________ > 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
