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Help on fetching an entry from swissprot ?

Reinhard Doelz doelz at comp.bioz.unibas.ch
Sun Feb 13 04:26:13 EST 1994


In article <2jjb6g$ju1 at threed.uchc.edu>, richk at mbcg.uchc.edu writes:
...
|> $ FETCH 
...
|>  FETCH what sequence(s) ?  sw:mbp_rat
|> 
|>  Mbp_Rat.Sw
|>  *** Sequence "Mbp_Rat.Sw" could not be read or is not in GCG format!
|> 
...

This might be that you find the entry correctly in the indices (otherwise
it wouldn't come back with the name Mbp_Rat.Sw but failed to extract 
it properly. Check 

$ show log swissprotdir

and then 

$ dir/date swissprotdir:sw*.seq
$ dir/date swissprotdir:sw*.names 

The idea is that .names and .offset files are used for retrieving 
the entry from the database. The dates of the names and offset 
files should be _LATER_ than the .seq and ref files as the indexing 
should have happened after the seq and ref file creation (see 
below). If the indices are copied from other computers, this 
argument might be weak. Then, you could try swissprot:calm_human 
(which is an entry in swissprot as well) in order to check whether 
swissprot is operable at your site at all. 


'yogi >  dir/date swissprotdir:sw*.seq

Directory BIOBIG:[BIOZEN.DATA.][GCGSWISSPROT]

SWISS.SEQ;1          12-NOV-1993 18:25:22.41

Total of 1 file.
'yogi >  dir/date swissprotdir:sw*.names

Directory BIOBIG:[BIOZEN.DATA.][GCGSWISSPROT]

SWISS.NAMES;3        12-NOV-1993 18:28:22.68

Total of 1 file.
'yogi >  dir/date swissprotdir:sw*.offset

Directory BIOBIG:[BIOZEN.DATA.][GCGSWISSPROT]

SWISS.OFFSET;3       12-NOV-1993 18:28:22.45

Total of 1 file.



--------

Forgive me to post the advertismenet in own matters here; 
but we have installed the Hierarchical Access System for 
Sequence Libraries in Europe (HASSLE) which is a (free) software
package for various tools. If there is a fault at a given database, 
or an entry is not found, our fetch behaves as the following 
(I have simulated a failure in swissprot due to bad indexing): 

'yogi >  fetch sw:mbp_rat

FETCH copies GCG sequences or data files from the GCG database
into your directory or displays them on your terminal screen.
... Trying Network ...Support data file is: "Support.Dat".
 Checking resources ...
....found database SW at YETI.EMBNET.UNIBAS.CH ..............
HFETCH HASSLE frontend R.Doelz Version 30/08/93 B4-0-0
--- HASSLE version B4-1-0pre4 (94/01/30) (C) Biocomputing Basel 1992-1994
NOTE: YETI.EMBNET.UNIBAS.CH is used as provider.
NOTE: Listening for reply from YETI.EMBNET.UNIBAS.CH on port 15020 for result
NOTE: Answer from host yeti.embnet.unibas.ch [131.152.8.3], port 2285 ...Resultfor service HFETCH

NOTE: Received file fetch.log

NOTE: Received file mbp_rat.sw
NOTE: JOB       15020    completed

This way, we can use a different computer and still get the 
correct answers even if the local one is temporarily out of data. 

Regards
Reinhard 




===============
DISCLAIMER
Note that  the software  mentioned  resembles  Computer  Program(s)  which 
require a license in order to be run unless stated otherwise in  a  state-
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tioned  within  a specific problem or example and must not be used to con-
clude that other  software products cannot possibly do a similar job. 

-- 
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  |      Biocomputing         | electronic Mail       doelz at urz.unibas.ch |
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