GAS and CEPH Database

Patricia Rodriguez-Tome tome at ebi.ac.uk
Thu Feb 16 07:23:22 EST 1995


Hello,

In article <D4278M.ro at news.cis.umn.edu>, dean at lenti.med.umn.edu (Dean Flanders) writes:
>Where can I get GAS, which is an affected pedigree member program I 
>believe. 

You can find this information in the BioCatalog maintained at the EBI.
(URL http://www.ebi.ac.uk/biocat/biocat.html)
Here is the corresponding entry :

AC             BC00116
NAME           GAS
DOMAIN         Genetic tools
DESCRIPTION    This package provides facilities for reading, writing,
DESCRIPTION    sectioning and performing statistical analyses on 
DESCRIPTION    phenotypic and genotypic data.
AUTHOR         Alan Young
RT             -
ADDRESS        Department of medicine at Oxford University (UK)
CONTACT        ayoung at vax.oxford.ac.uk
SITE           ftp anonymous well.ox.ac.uk
SITE           Directory /pub/genetics/gas
SITE-CONTACT   -
OS             DOS,SUN/Solaris, SunOS,DecAlpha(OSF1), Dec5000(ULTRIX)
LANGUAGE       C
VOLUME         -
REQUIRES       -

 In addition does anyone know where I can get the Unix version 
>of the CEPH database, I can only find the PC version.  I believe the Unix 
>version is Sybase orientated.

There is a Unix (Sybase) version of the database, but I don't know exactly
how it is distributed (I am enquiring).
The contact for the ceph database is : cephdbm at cephb.fr
The ascii files for the ceph db can be found at the ceph ftp server:
ftp.cephb.fr
directory : /pub/ceph_genotype_db/ceph_db/UNIX

here is part of the readme file
>
     -    ceph_db/UNIX/asc/ contains text files that represent all the
          concatenated markers and their genotypes for each chromosome.
          Read the ceph_db/UNIX/asc/Readme file to know what each line 
          of these files represents.
          To decompress these files use the following command:

                 uncompress chrii.asc.Z

              or uncompress *.asc.Z  ( to decompress several ...asc.Z files)

     -    In ceph_db/UNIX/link/ you will find for all markers in DB 7.1 
          the files in LINKAGE format. There is a chrii.pdi (for pedin.dat)
          and chrii.dti (for datain.dat) for each chromosome. To decompress
          these files, use the uncompress command.

                uncompress chrii.pdi.Z chrii.dti

     -    ceph_db/UNIX/mkr/ contains the list of all the markers in DB 7.1.
          This list is useful because it lets you know which marker number
          corresponds to which marker name. To decompress
          these files, use the uncompress command.

                 uncompress mk71.ii.Z


     -    In ceph_db/UNIX/lods/ you have the lod score table files 
          (lod scores for all marker pairs) for each chromosome.
          To decompress them use the uncompress command.

                 uncompress chrii.lods.Z



>Thanks!
>
>Dean
>

Regards,

Pat
-- 
=======================================================================
Dr. Patricia Rodriguez-Tome		| Email:tome at ebi.ac.uk
EBI - European Bioinformatics Institute	| URL:	http://www.ebi.ac.uk
Hinxton Hall, Hinxton			| Tel:	+44 (0)223 494 413
Cambridge CB10 1RQ, UK			| Fax:	+44 (0)223 494 468
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