MDL implemented the genome pipeline, designed and performed the analyses and drafted the manuscript.
A.E., B.M., J.M., and M.W.D. reviewed, annotated and performed data entry, editing, and data quality control for all prostate cancer references, G.Z., X.W., H.L. implemented the Genome Browser with the assistance of W.J., V.R., and S.T. and formatted and uploaded the ChromSorter PC.gff files.
Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve.wisc.edu/mauve
SGD first implemented the GBrowse genome viewer (http://browse.yeastgenome.org) on its website in 2004.
Our hypothesis that genomic RE landscapes are species/strain/individual-specific was implemented into the Genome Signature Imaging system to visualize and compute the RE-based signatures of any genome.
To implement the LR * SNP i ) test genome-wide, a sliding window approach was taken in which pairs of adjacent SNPs were used in (7).
Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale.
This orthology computation was based on that described and implemented for the genome sequence of Nematostella [ 30] with further refinement of the blocking rules.
Orthologs of TFs were identified by a procedure based on the analysis of phylogenetic trees for protein domains in MicrobesOnline [ 54] and validated by bidirectional genome-wide similarity searches with 30% of identity threshold using the Smith-Waterman algorithm implemented in the Genome Explorer program [ 58].
The latter methodology, sequencing-by-synthesis, is implemented in the Genome Sequencer GS-FLX System (454 Life Sciences), which produces several hundred thousand DNA reads of at least 200 bp; this is done by monitoring the release of pyrophosphate during the growth of a DNA chain driven by a DNA polymerase [ 6].
