E. coli Database Collection --> GCG format

David Konerding rafael at cse.ucsc.edu
Thu Nov 3 16:14:47 EST 1994


Peter Rice (pmr at staffa.sanger.ac.uk) wrote:
: In article <398sqb$79b at emory.mathcs.emory.edu> bcresas at bimcore.emory.edu (Scott Sammons) writes:
: >   Has anyone successfully reformatted the ECD data into GCG formatted databases.
: >   The program embltogcg core dumps when I try it with one of the ECD .dat
: >   files.

: As I am involved in both ECD and EGCG, I will try to put something into EGCG 8.0
: when it is ready. I take it you are referring to the very latest (new format)
: ECD here. Do you mean the genorf.dat file or the contigs/*.dna files (which are
: closer to EMBL format and have more sequence data)?

: Beware though - E.coli sequencing is now going so well that ECD has a contig (and
: more to follow) over the 350k mark, which will give some problems with GCG.

: Another option would be to use a script (or Perl) to reformat into enough of an
: "EMBL" format for EMBLtoGCG to accept it.

Hmm.  Can anybody give me a pointer to where I can find the ECD?  I am writing
a thesis which regards computational methods for finding genes in prokaryotic
DNA, and any database more complete than EcoSeq6 would be great.

Thanks.


: --
: ------------------------------------------------------------------------
: Peter Rice                           | Informatics Division
: E-mail: pmr at sanger.ac.uk             | The Sanger Centre
: Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
: Fax: (44) 1223 494919                | Cambs, CB10 1RQ
: URL: http://www.sanger.ac.uk/~pmr    | England

--
--
  O~_    -------------  David Konerding (University of California, Santa Cruz)
 c/ /'   -------        rafael at cse.ucsc.edu
( ) \( ) ---            rafael at cats.ucsc.edu





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