NBC (Neighborhood Breakpoint Conservation) is a method that identifies recurrent copy number variants in multiple individuals using Array Comparative Genomic Hybridization (aCGH).aCGH computes the ratio of test:reference DNA for probes located on the reference genome. NBC first uses a Bayesian changepoint algorithm to identify probes, called breakpoints, that change from low-to-high or high-to-low copy number with high probability. A binomial statistic is then applied to identify breakpoints and pairs of breakpoints that appear in a statistically significant number of individuals.
COMET (Cluster Of Motifs E-value Tool) finds statistically significant clusters of motifs in a DNA sequence. The motifs are represented using 4 x L matrices, which record the frequencies of the nucleotides A, C, G, and T at each position in the motif.
GASV / GASVPro (Geometric Analysis of Structural Variants) is a software for analysis of structural variation from paired-end sequencing and/or array-CGH data. This software has been tested used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format.
Lever systematically maps DNA regulatory motifs or motif combinations to the sets of genes that they likely regulate. Lever accomplishes this by assessing whether the motifs are enriched within cis regulatory modules (CRMs), predicted by our PhylCRM algorithm, in the noncoding sequences surrounding genes in a collection of gene sets.