New Software release : UNIX version of Genome Database Software Package

fw at sanger.ac.uk fw at sanger.ac.uk
Mon Jul 11 12:14:49 EST 1994



Software for genome mapping by fingerprinting techniques
--------------------------------------------------------

What it is 
-----------

A genome mapping package has been developed for reading and
assembling data from clones analysed by restriction enzyme
fragmentation and polyacrylamide gel electrophoresis. The
package comprises: data entry; matching; assembly; statistical
analysis; modelling. The Data is entered by a scanning and image
processing system, called IMAGE. The primary emphasis in the
analytical routines is on flexibility and interactive convenience, so
that the operator has full knowledge of and control over the
growing map, but a variety of automatic options are included. The
package continually grows to meet the needs of the Caenorhabditis
project. 

This software is the UNIX port of the CONTIG9 software package,
which was running on VAX/VMS only.
The Software announced here will run on a wide variety of
UNIX platforms, such as SUN-Sparc, SGI-Irix .
Binaries are provided for 

Where to find it
-----------------

The package is called ContigC and is available via
anonymous ftp on :
ftp.sanger.ac.uk:/pub/contigc/

You'll also find directories with precompiled binaries
and documentation files in HTML format (Mosaic browsable).

How to use it
--------------

(1) On-line documentation

A documentation is available on the InterNet. You have to use
Mosaic to browse the hypertext document.
Mosaic is available via anonymous ftp from :
ftp.ncsa.uiuc.edu:/Web/
src.doc.ic.ac.uk:/public/computing/information-systems/WWW/ncsa/

Type the following URL in the text window that comes up after
pressing 'o'-key in the Mosaic Window:
URL = "http://www.sanger.ac.uk/~fw/contigc.html"

This document will explain exactly, what the software does and how.


(2) locally installed Mosaic documents

For people with a slow InterNet connection to our server
there is a tarred archive of all HTML files and images,
which can be installed locally. This is on :
ftp.sanger.ac.uk:/pub/contigc/Doc-html/ContigC+IMAGE-HTML-doc.tar
(the file to start with is "index.html")

(3) documents ready to print in postscript

I created three postscript files from the HTML files. They are on :
ftp.sanger.ac.uk:/pub/contigc/Doc-postscript/*.ps

(4) pure text files without images

If neither Mosaic nor postscript programmes are available, pure
text files can be viewed in any ASCII editor. They're on :
ftp.sanger.ac.uk:/pub/contigc/Doc-text/*.txt


How to install it
------------------

I tried to make the installation as simple as possible.
A shell script reads the system configuration, calls
the make files and installs the programs after a successful
compilation. Type :

%  install

to start building the software.
It will then compile graphic-libraries, the image analysis
software and the database programs.




Note.:

 This is my last day at the Sanger Centre,
 I won't be available to answer questions or fix bugs
 until october, when I'll be at University.


------------------------------------------------------------
                  Friedemann Wobus

Email:    fw at sanger.ac.uk
WWW:      http://www.sanger.ac.uk/~fw

   The Sanger Centre       Tel:      +44 (0)223 834244
 Hinxton Hall, Hinxton     Fax:      +44 (0)223 494919
  Cambridge CB10 1RQ       WWW:      http://www.sanger.ac.uk




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