Users Guide for FISH Clones vs. Genomic Sequence Assembly Scatter Plots
| We give one plot for each chromosome that shows the data from the resource of FISH-mapped BAC clones (NCBI Clone Registry) placed on the working draft. These plots are at a fixed scale, so you will need to scroll right to cover the larger chromosomes. Another set of plots covers the genome in fixed scale 50mb windows, and a third set of plots covers the genome in 10mb windows. The position along the working draft sequence for the chromosome is plotted along the horizontal axis. Each cytogenetic band is allocated a height on the vertical axis, using the standard fractional lengths of the bands. A horizonal line is drawn across the plot at the height corresponding to the start position of each major band. The predicted location of every sub-band is shown by a light blue horizontal line segment that is located at the height corresponding to the midpoint of that sub-band, and positioned so that it begins at the horizontal coordinate predicted to be the beginning of the sub-band in the working draft sequence, and ends at the horizontal coordinate predicted to be the end of that sub-band in the working draft sequence. These predictions are calculated by a dynamic programming method described in "A Dynamic Programming Method to Locate Cytogenetic Bands on the Working Draft Sequence," and will be described more fully elsewhere. Each FISH-mapped clone is displayed as a point with error bars. The position of the point along the working draft sequence is determined using information about the clone, including STSs and BAC ends. The vertical position of the point is the midpoint in the range of possible bands predicted for the clone by FISH. The error bars indicate the range of uncertainty for the band location for the clone. The point is color-coded according to the lab that FISH-mapped the clone; see the key in upper right corner of the plot. Some clone markers are FISH-mapped to different chromosomes entirely. These are shown at the bottom of the display. ## Caveats: The cytogenetic band assignments by FISH have limited accuracy, for more details see "Integration of cytogenetic landmarks into the draft sequence of the human genome," by the BAC Resource Consortium, Nature, Vol. 409. The predictions of band positions by dynamic programming are subject to errors due to inaccuracies in the FISH data. They also rely weakly on approximations of the band sizes given by standard fractional band lengths, these can be very inaccurate and can vary between individuals, especially in the centromeric and telomeric regions.
Last modified: Fri Mar 22 13:25:52 PST 2002