E. coli Database Collection --> GCG format

Peter Rice pmr at staffa.sanger.ac.uk
Thu Nov 3 17:44:38 EST 1994


In article <39bjs7$t3p at darkstar.UCSC.EDU> rafael at cse.ucsc.edu (David Konerding) writes:
>   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)?
>
>   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.

The latest ECD is available from ftp.ebi.ac.uk in directory pub/databases/ecdc
(note the extra c at the end :-)

The new format is described in: Kroeger et al. (1994); Nucleic Acids Research 22:3450-3455.

The contigs directory has the non-redundant contiguous sequences from E.coli K-12.
--
------------------------------------------------------------------------
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




More information about the Bio-soft mailing list