ANNOUNCE: ICRF CONTIG-BUILDING PACKAGE, VERSION 2

Andrei Grigoriev andy at news.lif.icnet.uk
Fri Sep 16 14:22:29 EST 1994


			ANNOUNCEMENT
			============


		ICRF CONTIG-BUILDING PACKAGE 
		============================


			  VERSION 2
			  =========

			

		Richard Mott and Andrei Grigoriev,
		Genome Analysis Laboratory
		Imperial Cancer Research Fund
		44 Lincoln's Inn Fields
		London WC2A 3PX

		rmott at gea.lif.icnet.uk
		andy@@gea.lif.icnet.uk





We announce the release of version 2 of the ICRF contig-building
package. This is a suite of programs to aid the construction of
physical maps from hybridisation data. Most of the algorithms used by
the package are described in:-

Mott et al (1993)  ``Algorithms and software tools for ordering clone
libraries: appplication to the mapping of the genome of {\em
Schizosaccharomyces pombe}'',  Nucl. Acids Res.  21:1965-1974, and 

Grigoriev et al (1994), ``An algorithm to detect
chimeric clones and random noise in genomic mapping'', Genomics, 22:482-486



The programs are used routinely within our laboratory for the analysis
of mapping data from a variety of projects, including:

YAC, p1 and cosmid maps of S. pombe
YAC and cosmid pocket map of Human chromosome 21
YAC map of Human chromosome X



The programs are written in C (with some programs requiring the SUN
Xview graphics libraries).


		How To Get the Package
		======================


It can be obtained by anonymous ftp as the compressed tar file

icrf-public/GenomeAnalysis/icrf_contig_v2.tar.Z

from

ftp.icnet.uk



		New features:
		=============

Version 2 of this package contains some new programs and improvements
to existing ones.


CHIMAERA is a new program to filter noisy datasets, searching for
clones that are likely to be chimeric.

MUTUAL is a new program to clean up noisy datasets by searching for
mutually conststent hybridisation events.

OPENSEA is a new XView general-purpose program interface/file browser,
which enables the user to run the programs much more easily than
before.  It is configurable and can be adapted as an interface to any
program you would normally run from the command-line. For a full
description see the separate OpenSea Guide

SPAN is a new program to determine minimum-spanning sets of clones
 which cover a given order of probes.

WELL2CLONE is a new program for managing a database of hybridisation
data. 

SHOW can now produce colour PostScript files, which is useful for
highlighting particular probes and clones if you have a colour
printer.

PROBEORDER can now handle probes and clones with cytogenetic map
locations and can use an input set of contigs. It therefore has
superceded the old program contigorder

Various utility programs are included for the manipulation and
generation of the data files, including dumping data and maps into
ACeDB.







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