Journal Article

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

Alejandro A. Schäffer, Edward Stallknecht Rice, William Cook and Richa Agarwala

in Bioinformatics

Volume 23, issue 9, pages 1156-1158
Published in print May 2007 | ISSN: 1367-4803
Published online March 2007 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btm077
rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control

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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.

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

Contact: richa@helix.nih.gov, FAX: 301-480-2288. (Please send email concurrently with any fax.)

Journal Article.  2153 words. 

Subjects: Bioinformatics and Computational Biology

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