XQS errors with EMBL31, Genbank 72

MARZEC at GUNBRF.BITNET MARZEC at GUNBRF.BITNET
Tue Aug 4 08:53:00 EST 1992


ODONNELL at UK.AC.AFRC.ARCB (Cary O'Donnell) writes:
>           XQS, EMBL31, Genbank 72
>           =======================
>
>Has anyone else had the same problem with XQS version 3, EMBL31 and Genbank72?
>
>o The type and copy commands elicit the response that any given EMBL or Genbank
>  entry code is not in the database.
>
>  XQS> bases EMBL
>  XQS> type/text ebv
>  EBV cannot be found
>     The entry is not in the database
>
>o The author and keyword searches work OK and give a list of entries.
>  None of the entry codes reported can be typed or copied.
>
>o BUT ..... you can type the whole list!
>
>  XQS> author abe
>  .
>  .
>       27 authors found
>  XQS> list
>      149 entries on the current list
>  .
>  .
>  XQS> type/text
>  code:
>  current list entries will be processed
>  .
>  .
>
>  Then you DO get the text for the entries output.
>
>  Solutions to this problem welcomed. None of the smaller databases appear
>  to be affected - ie: PIR, Swissprot, daily EMBL updates.
>
>  Does anyone out there NOT get this with EMBL31? If so I must suspect my
>  index creation software, or XQS version3. I have run the index creation
>  twice now to make sure.
>
>Cary

Cary,

The problem you are experiencing with XQS is due to the large size of the
GenBank and EMBL databases when each is viewed as one database. XQS, as well
as PSQ and NAQ, uses a two byte variable for storage of entry codes and
therfore can access only upto ~65000 unique entries. The display commands
will not work with large datasets.

To fix this problem temporarily we split one of the larger of thirteen from
the main set (GBPRI.SEQ or PRI.DAT) and call this supplemental dataset
GENBANKSUP or EMBLSUP. The program GB_EMBL will do this; I will E-mail a
version of this program to you. Until further notice, this protocal must be
followed for all databases with totals exceeding 65000.

Regards,
Chris Marzec, PIR
MARZEC at GUNBRF.bitnet



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