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EPD/GCG

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Tue Mar 21 17:47:14 EST 1995


In <3kjs2g$7t6 at zaphod.crihan.fr> risler at cgmvax.cgm.cnrs-gif.fr writes:

> Does there exist somewhere a program that, starting from EPD, will
> generate a GCG-formatted databank? In other words, a program that will
> use the infos in EPD to fetch all the relevant items from EMBL and write
> them into a usable file? In this way I could run a FASTA against EPD ....

I have a program that does the following:
1.) Extracts EMBL sequence name and position of the transcription start from
    EPD based on a filter string specified by the user (e.g. PRI:HS)
2.) Converts the sequence name into GCG format (e.g. EM_PR:HS...)
3.) Calculates a /BEGIN and /END position based on the transcriptional
    start site indicated in the EDP and a shift specified by the user
4.) Composes a GCG-command out of the above together with a user defined string.

Example:
   If the sequence name is PRI:AGHBD and position is 235. Then the program
   could write a line like

   $ ASSEMBLE/NOMONITOR/DEFAULT EM_PR:AGHBD /BEGIN=1/END=335/OUT=AGHBD_235.X ! Ag d'globin         

   and repeat this step for all entries that fit into the filter criteria.
   "$ ASSEMBLE/NOMONITOR/DEFAULT" is the template provided by the user,
   input file and output file are derived from the EDP, /BEGIN and /END are
   calculated according to EPD and a shift entered by the user (here -500 +100).

If there is enough demand I'll post the file with all the 1251 lines.

Regards,
   Christoph Gartmann


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