[EMBOSS] retrieving entries from public database
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 EMBOSS is so out-of-date that I cannot follow it.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 [
fields: "id acc gi sv des org key"
2)Save the emboss.default and make sure you have your Internet
3)Test your 'special' set with a query from the command line:
This should do the trick.
Senior Systems Engineer/IT Manager
Biotek Center, University of Oslo
EMBnet TMPC Chair
Tel: +47 22840535
More information about the EMBOSS