Applications that require resequencing of hundreds or thousands of predefined genomic regions in numerous samples are common in studies of non-model organisms. However few approaches at the scale intermediate between multiplex PCR and sequence capture methods are available. Here we explored the utility of Molecular Inversion Probes (MIPs) for the medium-scale targeted resequencing in a non-mode...

Customers arrive to a single service queue according to a Poisson process with rate l, from which they are routed to two parallel heterogeneous and exponential servers whose ra.tes are 1'1 > #2· Customers are released from the system after service completion, according to their arrival order a requirement introducing additional resequencing delays. Customers which are delayed due to resequencin...

Oligonucleotide microarrays offer the potential to efficiently test for multiple organisms, an excellent feature for surveillance applications. Among these, resequencing microarrays are of particular interest, as they possess additional unique capabilities to track pathogens' genetic variations and perform detailed discrimination of closely related organisms. However, this potential can only be...

This kit was developed for BESC genome resequencing projects. The target for resequencing is usually the genome of a strain, which is further referred to as the mutant strain, or M strain, with a practically important phenotype evolved by an adaptation of a wild type strain. This phenotype is absent in the wild type strain, or WT strain, with a completely sequenced genome, which is used as the ...

The availability of multiple genome-wide human polymorphism datasets has led to an increase in efforts to scan the genome for signals of positive selection. As a result, the number of loci in the human genome predicted to be adaptively evolving increases monthly. Yet, these numerous genome-wide scans have identified minimally overlapping sets of candidate loci, potentially due to biases in geno...

Recent exponential growth in the throughput of next-generation DNA sequencing platforms has dramatically spurred the use of accessible and scalable targeted resequencing approaches. This includes candidate region diagnostic resequencing and novel variant validation from whole genome or exome sequencing analysis. We have previously demonstrated that selective genomic circularization is a robust ...

Resequencing microarrays are a common tool for fast monitoring of individual genetic variations. Applications include diagnosis of genetic and infectious diseases and SNP prediction. Base calling is the crucial step in the analysis of resequencing data. All current base calling algorithms produce ambiguous calls on parts of the sequence. Therefore, proper data handling, editing and visualizatio...

High-throughput pooled resequencing offers significant potential for whole genome population sequencing. However, its main drawback is the loss of haplotype information. In order to regain some of this information, we present LDx, a computational tool for estimating linkage disequilibrium (LD) from pooled resequencing data. LDx uses an approximate maximum likelihood approach to estimate LD (r(2...

Rare genetic variants, identified by in-detail resequencing of loci, may contribute to complex traits. We used the apolipoprotein A-I gene (APOA1), a major high-density lipoprotein (HDL) gene, and population-based resequencing to determine the spectrum of genetic variants, the phenotypic characteristics of these variants, and how these results compared with results based on resequencing only th...

SUMMARY Because an enormous amount of sequence data is being collected, a method to effectively display sequence variation information is urgently needed. tasuke is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and read depths of multiple genomes,...