Cytogenetic Bands
| # A Dynamic Programming Method to Locate Cytogenetic Bands on the Working Draft Sequence Terrence Furey, Wonhee Jang, Arek Kasprzyk, Ewan Birney, Greg Schuler, Vivian Cheung, Barbara Trask, David Haussler UCSC, NCBI, EBI, EBI, NCBI, Children's Hospital of Philadelphia, Fred Hutchinson Cancer Research Center, HHMI/UCSC Advances in Genome Biology and Technology, February 3-6, 2001, Marco Island Resort & Golf Club We have developed a dynamic programming algorithm that predicts the locations of chromosomal bands and sub-bands on the working draft genome sequence using FISH-mapped clones. The BAC Resource Consortium [1] has located positions on the Sept. 5 working draft genome sequence at http://genome.ucsc.edu for 7364 clones that have been mapped by FISH to particular cytogenetic bands or ranges of bands. This is the primary data used by the algorithm. The algorithm predicts band locations in the genome sequence so as to maximize the number of clones from this data set that lie in the bands predicted by FISH, subject to the constraint that the bands must appear in the correct order and their sizes cannot deviate greatly from their standard fractional sizes. In cases of contradictory data, higher weight is given to higher resolution FISH data. In the absence of FISH data, sub-band sizes are optimally fit to the standard fractional sizes. The resulting band predictions can be used to help locate genes of clinical and scientific significance in the working draft, and also to study properties of the sequence that are associated with cytogenetic banding. [1] BAC Resource Consortium, Navigating from chromosomal abberations to genes: linking the cytogenetic and sequence maps of the human genome, Nature, Vol. 409.
Last modified: Fri Mar 22 13:31:13 PST 2002