Skip Navigation


Bioinformatics Advance Access originally published online on March 1, 2007
Bioinformatics 2007 23(9):1156-1158; doi:10.1093/bioinformatics/btm077
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
23/9/1156    most recent
btm077v2
btm077v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (11)
Google Scholar
Right arrow Articles by Schäffer, A. A.
Right arrow Articles by Agarwala, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Schäffer, A. A.
Right arrow Articles by Agarwala, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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 1, Edward Stallknecht Rice 1,2, William Cook 3 and Richa Agarwala 1,*

1National 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, 2Thomas Jefferson High School for Science and Technology, 6560 Braddock Road, Alexandria, VA 22312 and 3Industrial and Systems Engineering, Georgia Tech, 765 Ferst Drive, Atlanta, GA 30332, USA

*To whom correspondence should be addressed.


  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.

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{at}helix.nih.gov, FAX: 301-480-2288. (Please send email concurrently with any fax.)

Associate Editor: Alex Bateman

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.