HUMAN CHROMOSOME 22 ACEDB DATABASE

Ian Dunham id1
Mon Aug 21 12:21:14 EST 1995


==================================

			HUMAN CHROMOSOME 22 ACEDB DATABASE

			==================================


The first release of the human chromosome 22 physical mapping database (22ace) 
from the Sanger Centre is now available by ftp from ftp.sanger.ac.uk in directory
pub/human/chr22/physical_map.  The database is implemented in version 4_1 of ACEDB, 
the graphical database manager, developed for the nematode genome project.  

The database includes all the YAC and cosmid physical map data from the Sanger Centre 
chromosome 22 mapping group, presented in context with reagent details, relevant DNA 
sequences, bibliography, and so on.  We are using the database to store the information
generated as the Sanger Centre's part of a joint project to sequence chromosome 22
and further releases will present physical map and sequence progress, in its full
genomic context.  

Details of how to obtain the database, and more description of its contents are 
contained in the README file which is included below. 

Many thanks go to the following for their work in helping to get this database 
together, 

The Sanger Centre chromosome 22 mapping group - John Collins, Charlotte Cole, Luc
Smink, Charmain Garrett, Kathy Evans, Joanne Fay, Lisa O'Neill, Margaret Leversha,
Simon Gregory.

Gareth Maslen, Kate Rice, Richard Durbin, Simon Kelley and Cari Soderlund on informatics.

Callum Bell, Bruce Roe, Tom Hudson and all those at the Philadelphia and Whitehead Institute 
genome centers for provision of data.

For further information, please feel free to contact Ian Dunham at

--------------------------------------------------------------------------
\
// Ian Dunham					Tel:  01223 494948
\  Sanger Centre				FAX:  01223 494919
// Hinxton Hall
\  Hinxton
// Cambridge				Email:	id1 at sanger.ac.uk
\  CB10 1RQ					idunham at hgmp.mrc.ac.uk
// 					www: http://www.sanger.ac.uk/~id1
==========================================================================


README File
-----------

This is the release version of the human chromosome 22 version of ACEDB.
The database uses the current release of the ACEDB code, ACEDB 4_1 which
can also be obtained independently from this site in directory pub/acedb.

The database contains 

	-  The YAC physical map of chromosome 22 as determined by the chromosome 22 mapping group
	at the Sanger Centre

	-  Current progress on cosmid mapping and sequencing from the Sanger Centre

	-  YAC/STS assignments from the Philadelphia Genome Center and the Whitehead Institute as
	described in Bell et al.,  Hum Mol Genet 4, 59-69 (1995) and Hudson et al., Genomics
	24, 588-592 (1994) - Thanks to Callum Bell and all those at these institutes for providing
	these data in electronic form.  See also their WWW sites as detailed in the database for 
	more information.  

	-  Current progress on cosmid mapping and sequencing from the Sanger Centre

	-  Information on all probes and STS markers used in the YAC map plus many others

	-  DNA sequences from chromosome 22 including cosmid from the Sanger Centre submitted to
EMBL

	-  Representations of genetic maps of the chromosome and hybrid mapping data, including bin
	assignments from The Philadelphia Genome Center and the Whitehead Institute (Bell et al.,  
	Hum Mol Genet 4, 59-69 (1995) and Hudson et al., Genomics 24, 588-592 (1994) and hybrid data 
	generated at the Sanger Centre

	-  An extensive bibliography

	-  Addresses of laboratories involved in chromosome 22 mapping

	-  Representations of the CEPH mega, ICRF and ICI YAC libraries, and the flow sorted 
	chromosome 22 cosmid library (LL22NC03) 

	-  OMIM data on diseases and loci on the chromosome

	
To use the database get the file 22db.tar.Z by ftp.

Uncompress the file in the directory of your choice - I suggest your root 
directory.  i.e.

> uncompress 22db.tar.Z

then extract the tar file to form a subdirectory tree rooted on the 
directory 22db. i.e. 

> tar -xvf 22db.tar

In the directory 22db/bin you will find subdirectories containing 
binary executables for DEC ALPHA, SunOS, Solaris and SGI.  To run the database
set the environment variable ACEDB to the directory 22db i.e. 

> setenv ACEDB 22db

and run the executable you require i.e. for DEC ALPHA

22db/bin/ALPHA/ace4_1.ALPHA 

The database should now run.  It is possible to run the same database from 
machines with the different operating systems and to have a script to do this.
Here is an example of a script we use where the database is held in directory
~id1/22db.

-----------------------------begin script----------------------
#!/bin/csh

setenv ACEDB ~id1/22db
echo -n "ACEDB home directory : "
echo $ACEDB
echo

switch (`ostype`)
  case "OSF1":
       ~id1/22db/bin/ALPHA/ace4_1.ALPHA
        breaksw
  case "SunOS":
        ~id1/22db/bin/SunOS/ace4_1.SUN
        breaksw
  case "Irix":
        ~id1/22db/bin/SGI/ace4_1.SGI
        breaksw
  case "Solaris":
        ~id1/22db/bin/SOL/ace4_1.SOLARIS
        breaksw
endsw

----------------------------end----------------------------------

To view the physical map of the chromosome double click on Maps and
the full YAC map will be presented in scrollable form.

I should stress that this is a direct copy of the laboratory database we use 
and as such may not contain some of the information you deem necessary.  
Please feel free to send me comments so that I can improve the database and
correct any mistakes. If you need further information about the final release 
please contact me as well. 

Also included in the directory pub/human/chr22/physical_map/sam are
the sam solution files that we used to construct the YAC map.  To use these
you must also pick up the latest version of the program sam, written by 
Cari Soderlund, from the directory pub/sam (At least version 2.5 is required).

--------------------------------------------------------------------------
\
// Ian Dunham					Tel:  01223 494948
\  Sanger Centre				FAX:  01223 494919
// Hinxton Hall
\  Hinxton
// Cambridge				Email:	id1 at sanger.ac.uk
\  CB10 1RQ					idunham at hgmp.mrc.ac.uk
// 					www: http://www.sanger.ac.uk/~id1
==========================================================================


Ian Dunham
21 August 1995





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