NCBI Integrated Radiation Hybrid Map
 Chrs: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X

  Human Genome Resources

 

The chromosome maps on these pages were computed as described in the manuscript:

R. Agarwala et al., A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy. Genome Research 10:350-364 (2000).
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The maps represent our effort to integrate subsets of markers from the GB4 and G3 panel maps previously produced. The radiation hybrid vector data was downloaded from RHdb. We recomputed maps for GB4 and G3 panel markers using a new strategy for selecting framework markers and a new strategy for constructing maps using existing software for the Traveling Salesman Problem, namely CONCORDE.

We demonstrated that these maps are better than existing maps by the standard criteria of maximum likelihood and minimum obligate chromosome breaks and by comparison with sequence data submitted to GenBank. We then developed and implemented a strategy for integrating the new GB4 and G3 panel maps based on known methods for the Longest Common Subsequence problem.

For each chromosome, the recomputed integrated map has columns for
(i) marker name,
(ii) position (cR) on the integrated map,
(iii) LOD score comparing best position to next best position on the integrated map,
(iv) position (cR) on the recomputed GB4 map,
(v) LOD score comparing best position to next best position on the recomputed GB4 map,
(vi) position (cR) on the recomputed G3 map, and
(vii) LOD score comparing best position to next best position on recomputed G3 map.

The odds for a positional assignment are 10 raised to the LOD score to 1. For example, a LOD score of 4.0 corresponds to odds of 10,000:1.

When multiple consecutive markers are assigned to the same position, this means that the markers belong to what we call an "extendible piece" of the sequence of markers, and that "extendible piece" cannot be consistently oriented either from top to bottom or bottom to top. Multiple markers with the same position does not necessarily mean that the markers have identical radiation hybrid vectors.

The software used to construct the new maps is freely available by sending e-mail to Dr. Richa Agarwala at agarwala@ncbi.nlm.nih.gov. Also send any questions and comments about the maps to Dr. Agarwala.

 

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