bioftp EMBL/GENBANK server update

doelz at comp.bioz.unibas.ch doelz at comp.bioz.unibas.ch
Thu May 7 10:30:32 EST 1992


On the bioftp server there is a new directory which 
contains all GENBANK.71 entries not in EMBL at  the 
1st of May, 1992. Look in the directory 

biology/EMBnet/database/genbank_suppl 

to find PIR/GCG ASCII-formatted data in .ref , .seq 
and .header format  suited  for both  VMS  and UNIX 
formatting in GCG software with the dbindex program. 
Note that you have to convert the ftp'ed  files  in 
VAX/VMS as described below. 

All daily updates from EMBL since release 30 are in 

biology/EMBnet/Xembl_flat

in EMBL flat file format. The XEMBL  files  contain
entries NEW in the release 31, whereas  the  XXEMBL 
data contain data which are modified and have  been 
already in release 30 or ealier. The PIR/GCG ASCII-
formatted files in .ref , .seq and  .header  format  
suited  for both  VMS and UNIX are in the directory

biology/EMBnet/Xembl_form 

and can be handled as described below. There  is  a 
new directory called 

biology/EMBnet/gb_non_xembl

which contains  WEEKLY  updates  from  NCBI-genbank 
as assembled from the  update  file.  Entries  with 
accession numbers found already in XEMBL and XXEMBL 
have been excluded.The updates are ftp'ed from NCBI
each saturday. 


Procedure to index the data for GCG Version 7 after 
ftp'ing follow. 

1) UNIX operating system 

#!/bin.csh
gcg
foreach i (*.seq)
   dbindex $i
end

2) VMS  operating system  (Be sure to have the file 
vms.fdl  (conversion) in your directory as found in 
biology/EMBnet/vms.fdl)

$! dcl script
$ gcg
$ next:
$       f = f$search ("*.*")
$       write sys$output f
$       if (f .eqs. "") then goto next2
$       convert/fdl=vms.fdl 'f' 'f'
$       purge
$       goto next
$ next2:
$       f = f$search ("*.seq")
$       if (f .eqs. "") then exit
$       dbindex 'f'
$       purge
$       goto next

Regards 
Reinhard 



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