IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

General error or specific for my setup?

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Wed Jan 10 09:15:36 EST 1996

In <4d05bf$i4 at rc1.vub.ac.be> gbottu at ben.vub.ac.be writes:

> I have found the cause of the problem at the BEN site : The EMBL has 3
> sequences of more than 350000 bases long and from GCG 8.1 on, the way
> GCG splits these sequences has changed. To allow SRS to recompose the
> sequences, I modified the file srsgeneral.sdl, I replaced
> ! gcg sequence file
> #filetype /ID=%GCGSEQ_FILE
>           /typename=seq /maxline=20000
>           /begstr=">>>>" /advance=0 /exitstr=">>>>"
>           /find=id /iscont="-"
> by
> ! gcg sequence file
> #filetype /ID=%GCGSEQ_FILE
>           /typename=seq /maxline=20000
>           /begstr=">>>>" /advance=0 /exitstr=">>>>"
>           /seqtype=gcg8_1
> I had not reindexed. Changing srsgeneral.sdl back to its old form
> cures the problem of the faulty sequence retrieval, except of course
> that the long sequences are not handled well.
> I do not know if remaking all the indexes after the change would have
> helped (since this takes a whole weekend, I did not try it just now).
> I also have no idea if the problem of Christoph Gartmann has the
> same cause or is entirely different.

All my indices were created with /seqtype=gcg8_1 . Now I changed the SDL back
to its original state and I experience the same as Guy. So I think reindexing
won't help, it is more a matter of a correct SDL. 

   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           |
| D-79011  Freiburg, FRG                                                     |
+----------- Do you know MENUE, the user environment for OpenVMS? -----------+

More information about the Bio-srs mailing list

Send comments to us at archive@iubioarchive.bio.net