[EMBOSS] retrieving entries from public database

Georgios Magklaras georgios at biotek.uio.no
Sun Aug 8 20:56:18 UTC 2010

  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 EMBOSS is so out-of-date that I cannot follow it.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


Tel: +47 22840535

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