The development of Next Generation Sequencing technologies, capable of sequencing hundreds of millions of short reads (25-70 bp each) in a single run, is opening the door to population genomic studies of non-model species. In this paper we present SHRiMP - the SHort Read Mapping Package: a set of algorithms and methods to map short reads to a genome, even in the presence of a large amount of po...

During the last three decades, both genome mapping and sequencing methods have advanced significantly to provide a foundation for scientists to understand genome structures and functions in many species. Generally speaking, genome mapping relies on genome sequencing to provide basic materials, such as DNA probes and markers for their localizations, thus constructing the maps. On the other hand,...

In order to perform breeding programs and improve production of native chickens, preserving genetic diversity in different areas of Iran is important due to the reduced available population. Genome sequencing is considered the most functional approach to determine the phylogeny relation between close populations. The aim of the present study was the evaluation of the phylogeny and genetic nucle...

Inference of population structure and individual ancestry is important both for population genetics and for association studies. With next generation sequencing technologies it is possible to obtain genetic data for all accessible genetic variations in the genome. Existing methods for admixture analysis rely on known genotypes. However, individual genotypes cannot be inferred from low-depth seq...

The recent development of homologous recombination-mediated gene targeting (GT) techniques has made it easy to modify nucleotide sequences in plant genomes. Backcross breeding following GT provides transgene-free lines with high probability. However, owing the possibility unintentional transgene introduction during genetic transformation, analytical methods may be necessary reliably and compreh...