Contig Ordering Package

This package was designed to allow the ordering of YAC ( Yeast Artificial Chromosome ) contigs but has recently grown into a general purpose genetic physical mapping program. It orders data from a small number of probes on small YAC contigs, to whole chromosomes of more than 1000 markers, using YAC and RH ( Radiation Hybrid ) data and including the integration of multiple 3rd party maps ( like the CEPH genetic map ). It includes many graphical data visialization tools, an assortment of search functions, scripting language, and a menu-driven user interface.

co2 program screenshot

features:

  • Orders genetic probes ( STS's ) up to several thousand per chromosome or more!
  • Considers YAC and RH data.
  • Integrates any number of 3rd party maps.
  • Menu-driven user interface
  • Fully scriptable with the TCL programming language
  • View YAC, RH and map data on a large matrix type display. Display weak linkage areas, 'floating' markers, and 'mapped' markers.
  • Compare proposed final order against other maps.
  • Compare various runs of the same stochastic search algorthim for differences in conversion using a 'Searls Map' type display.
  • For HMM data, view the alignment of HMM bins.
  • Assortment of search algorithms: Simulated annealing, greedy search, rippling windowed searches and other wierd and effective search algorithms.
  • Assortment of cost functions: RH and YAC cost functions, map violation cost functions, non-linear gap length minimization... even HMM cost functions.
  • All cost functions may be combined with a linear weighted cost function.
  • Calculates and displays doubly linked contigs.
  • Flexible and modular search code may be easily integrated into other programs.
  • Includes the Whitehead Institute's new 10000 marker human genome physical map.

    • availability:

    There are two versions available, a very small and simple early version and a larger more complete version. The graphical version comes with a menu driven graphical interface as well as a text based scripting interface and more mapping algorithms. The older smaller version is available because it is simpler and may be ideal for solving smaller mapping problems.

    Both versions require GCC 2.7.0 or better, and the graphical version requires TCL/TK 7.4 or better. It has been compiled and run on Sun4, Solaris and ALPHA workstations. The FTP package now comes with autoconf for easier installation. If you download this please send me an email, and I'll help you get it going.

    You may preview the documentation for co2 here.