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Bioinformatics Advance Access first published online on March 1, 2007
This version published online on March 2, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm077
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

rh_tsp_map 3.0: End-to-end radiation hybrid mapping with improved speed and quality control

Alejandro A. Schäffer a, Edward Stallknecht Rice a,b, William Cook c and Richa Agarwala a,*

a National Center for Biotechnology Information; National Institutes of Health; Department of Health and Human Services; Bldg. 38A, Room 10-03N; 8600 Rockville Pike; Bethesda, MD 20894 USA;
b Thomas Jefferson High School for Science and Technology, 6560 Braddock Road; Alexandria, VA 22312 USA;
c Industrial and Systems Engineering; Georgia Tech; 765 Ferst Drive; Atlanta, GA 30332 USA

*to whom correspondence should be addressed. Dr. Richa Agarwala, E-mail: richa{at}helix.nih.gov


  Abstract

Summary: rh_tsp_map is a software package for computing radiation hybrid (RH) maps and for integrating physical and genetic maps. It solves the central mapping instances by reducing them to the traveling salesman problem (TSP) and using a modification of the CONCORDE package to solve the TSP instances. We present some of the features added between the initial rh_tsp_map version 1.0 and the current version 3.0, emphasizing the automation of many steps and addition of various checks designed to find problems with the input data. Iterations of improved input data followed by fast re-computation of the maps improves the quality of the final maps. contain at least one 2.

Availability: rh_tsp_map source code and documentation including a tutorial is available at ftp://ftp.ncbi.nih.gov/pub/agarwala/rhmapping/rh_tsp_map.tar.gz. CONCORDE modified for RH mapping is available in the directory http://www.isye.gatech.edu/~wcook/rh/. The QSopt library needed for CONCORDE is available at http://www2.isye.gatech.edu/~wcook/qsopt/downloads/downloads.htm.

Associate Editor: Dr. Alex Bateman

Received on January 19, 2007; revised on February 26, 2007; accepted on February 26, 2007

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