The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations.

BACKGROUND: The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes. RESULTS: We demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses. CONCLUSION: This software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.

Bayesian inversion of reverberation and propagation data for geoacoustic and scattering parameters.

This paper applies nonlinear Bayesian inference theory to quantify the information content of reverberation and short-range propagation data, both individually and in joint inversion, to resolve seabed geoacoustic and scattering properties. The inversion of reverberation data alone is shown to poorly resolve seabed properties because of strong multi-dimensional correlations between parameters. Inversion of propagation data alone is limited by different correlations, but better constrains the geoacoustic parameters. However, propagation data are insensitive to scattering parameters such as Lambert's scattering coefficient. In each case the parameter correlations are inherent in the physics of the forward problem (reverberation and propagation) and cannot be overcome by processing or inversion techniques; rather, the inversion of more informative data is required. This is accomplished here by joint inversion of reverberation and propagation data, weighted according to their respective maximum-likelihood error estimates. Joint inversion of reverberation and propagation data collected on the Malta Plateau (Strait of Sicily) resolves both geoacoustic and scattering properties and achieves smaller uncertainties for all parameters than obtained by the inversion of either data set alone.

Target detection and location with ambient noise.

By placing a vertical array in an ambient noise field and forming an upward and a downward beam one obtains two time series which can be cross correlated to reveal a subbottom profile of the seabed [Siderius et al., J. Acoust. Soc. Am. 120, 1315-1323 (2006)]. Here the cross-correlation approach is applied to the location in range and bearing of a point target. An experiment was designed using floats and weights mounted (and dismounted) on the same cable as the vertical array. Careful measurements were made of the location of all likely floats, ballast weights, array terminations, and so on. After suitable coherent averaging, peaks were seen at delays (correlation offsets) agreeing with the reflector positions and were shown to be absent when reflectors were removed. A trivial extension of the theory developed in Harrison and Siderius [J. Acoust. Soc. Am. 123, 1282-1296 (2008)] is used to explain the rough amplitudes of the reflections. The approach differs from "acoustic daylight" principally in having a capability to determine a target range.