SRS and GCG databases

Guy Bottu gbottu at bigben.vub.ac.be
Tue Dec 5 09:32:56 EST 2000


	Dear Krishna,

Using databanks in GCG instead of "native" format is in principle not
complicated. Under SRS 6 you must in the file xxx.i change two things :
replace :
  fileType:{$DAT_FILE $SEQ_FILE} #orig format
  #  fileType:{$GCGREF_FILE $GCGSEQ_FILE} #GCG format
by :
  #  fileType:{$DAT_FILE $SEQ_FILE} #orig format
  fileType:{$GCGREF_FILE $GCGSEQ_FILE} #GCG format
and replace :
    #    $Field:[$DF_DNASequence token:gcgseq format:embl] #GCG format
    $Field:[$DF_DNASequence token:sequence format:embl] #orig format
by :
        $Field:[$DF_DNASequence token:gcgseq format:embl] #GCG format
    #$Field:[$DF_DNASequence token:sequence format:embl] #orig format

Under SRS 5 it is similar, except that the distribution files are
already configured for GCG databanks. Make of course sure that the path
in srsdb.i and the file name in xxx.i are correct.
There is however a problem : we are using SRS 6.0.7.2 at the moment and
I have noticed that for databanks in GenBank format (GenBank, Genpept,
Aidsbase,...) SRS cannot index the GCG version. We'll see what SRS
6.0.7.3 does.

	Guy Bottu








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