[EMBOSS] retrieving entries from public database

Hanquan Liang hliang at ksu.edu
Sun Aug 8 22:49:17 UTC 2010


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
<georgios at biotek.uio.no> 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 EMBOSS is so out-of-date that I cannot follow it.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
> EMBOSS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/emboss

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