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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.

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


   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.

   Christoph Gartmann

| Max-Planck-Institut fuer      Phone   : +49-761-5108-465   Fax: -221       |
| Immunbiologie                 PSI     : PSI%(0262)45050160374::GARTMANN    |
| Postfach 1169                 Internet: gartmann at immunbio.mpg.de           |
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