GRIMM

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Human, cat, mouse gene data from Bill Murphy

by Glenn Tesler

The raw data for the human, cat, mouse comparisons is in the Excel Spreadsheet LocusList101399.xls, provided by Bill Murphy, who was then at the National Cancer Institute (now at Texas A&M).

Guillaume Bourque identified common markers, either in all three species, or in pairs of them, and assigned consecutive numbers 1, 2, ..., n to the markers in each comparison. The spreadsheet does not contain information giving the direction (sign) of each gene. His programs assign signs to genes if there are blocks of consecutive genes conserved among the genomes, and discards other genes. GRIMM implements the Hannenhalli and Pevzner algorithm for unsigned genomes to determine an optimal assignment of signs, and Tesler's extension of this to multichromosomal genomes; however, when the data is too complex, obtaining an exact answer can be time consuming or impossible.

 

Human/Cat Data (193 genes)

Bourque identified 193 common markers among the three genomes human, cat, mouse; here are their descriptions.

It took 27 minutes for GRIMM to compute optimal signs, so our demonstration data (available on a menu on the GRIMM web page) includes the computed sign information that was not present in the experimental data.

 

Human/Mouse Data (123 genes)

The human/mouse and cat/mouse data were too complex to determine optimal signs using our current algorithm. We plan to work on improvements to the algorithm or our implementation of it. Meanwhile, we provide this data with a subset of 123 genes whose signs can be determined; here are their descriptions.

This page was created by Glenn Tesler, University of California, San Diego.