Population genetic statistics were generated using the compute program included with the libsequence library (Hudson et al. 1992; Thornton 2003).
GO terms containing a significant over-representation of promoters with two fold HNF4α enrichment in the ChIP-chip analysis were identified using Fishers Exact Test, which was performed using the statistical computing program package R http://cran.r-project.org/.org/
Using the computed HMM, the program iteratively searches a database of profile HMMs, with similar HMMs used to update the query HMM.
The paper describes this implementation using the Compute Unified Device Architecture programming environment, and demonstrates its advantages in GPU performance compared to GPU implementation of Real-Time Adaptive A*.
For this purpose we used the strph2 program, which computes Rosyton's modification of O'Quingley, Xu and Stare's modification of Nagelkerke's coefficient of determination for survival models [ 17, 18].
We used the BROMOC program suite to compute ion conductance with Grand-Canonical Monte Carlo simutilizingutilizing an algorithm of Im, Seefeld, and Roux.
In addition, we used the melting program (Novère, 2001) to compute the melting temperature between the predicted primer and its complement from the target sequence.
We used the Allegro program [ 10] to compute haplotypes as well as two-point and multipoint logarithm of the odds (LOD) scores, under the assumption of autosomal dominant inheritance with 100% penetrance, and with the disease-allele frequency set at.0001, and equal marker allele frequencies.
I used the program PLINK to compute observed and expected heterozygosity per locus in the subset of 17 northeastern and Ohio coyotes.
To derive an efficient mapping onto this type of computer architecture, we have used the new Compute Unified Device Architecture programming interface to implement a new parallel algorithm.
