Antwort: [EMBOSS] Can't connect internal SRSWWW ver7

[David.Bauer at schering.de]

Hello Akira,

one answer and one more question (I guess Peter is listening :-)

In your emboss.default the database name is GENBANK. (DB GENBANK)
So you must use GENBANK:AB001611 to get the sequence.
The dbalias specifies the name of the database within SRS. This is used to
formulate the wgetz request.
If you want to query more than one database you can put the list in this
place.
In SRS GenBank and RefSeq are separate databases.
So I use dbalias: "{genbank%20refseq}"
If it still does not work use -debug. Seqret (like all other emboss
programs) then writes a file seqret.dbg which contains the complete
communication log of seqret with the srs server.

Hope this helps,
David.

And now my question to Peter:
I would like to use in fields also the GI number.
In ajsrsdb I see queries for sv, org, des etc.
But even if I specify this in fields of emboss.default the SRS request is
only for ID and ACC.
So what to do, if I want to be able to retrieve by SV ?




Dear EMBOSS users

 I would like to ask a very primitive question.
I installed EMBOSS 2.8 on linux environment and we have SRSWWW internally
on other host machine without proxy configuration.
Our emboss.default file is vary simple as follows.
##############
DB GENBANK [ type: N method: srswww format: genbank
             url: http://hostname:8080/srs71bin/cgi-bin/wgetz
             dbalias: GENBANK
             fields: "sv des org key"
             comment: "Genbank IDs"
             ]
#############
But, when I typed
seqret -sequence DDBJ:AB001611 -outseq AB001611.fasta -osformat fasta
machine returns
Reads and writes (returns) sequences
Error: failed to open filename 'DDBJ'
Error: Unable to read sequence 'DDBJ:AB001611'
Died: seqret terminated: Bad value for '-sequence' and no prompt

I can't specify which process has  the issue for connecting with SRS. If we
tried to jump to internet SRSWWW , we need proxy with user authentication,
so it is difficult to verify with other outer resources in current EMBOSS
version. The possibility could be

(1)EMBOSS can't recognize SRS7??
(2)Some configuration trouble in emboss.default file
and others.......

But anyway, I would like to know which process has the issue for retrieving
sequence from SRSWWW. How can I see that??
Any suggestions will be highly welcomed.


Regards,

                   Akira Onozuka

#####################################################
Shionogi & Co., Ltd
12-4, Sagisu 5-chome, Fukushima-ku, Osaka 553-0002, Japan
Sr.Research Scientist
TEL:+81-6-6455-2015　　FAX :+81-6-6455-2066
E-mail  akira.onozuka at shionogi.co.jp
#####################################################