.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90

substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for insertion and deletion events in addition to substitutions, given a phylogenetic tree, using a rate matrix augmented by the gap character. Starting from a continuous Markov process, we construct a non

Abstract. Comparison of sequences that have descended from a common ancestor based on an explicit stochastic model of substitutions, insertions and deletions has risen to prominence in the last decade. Making statements about the positions of insertions-deletions (abbr. indels) is central

estimate the number of distinct values. The samples can be incrementally maintained up-to-date in the presence of data insertions and deletions, with minimal time and memory overheads, so that the full scan may be performed only once. Moreover, a stored Distinct Sample can be used to accurately estimate

We develop several analytical lower bounds on the capacity of binary insertion and deletion channels by considering independent uniformly distributed (i.u.d.) inputs and computing lower bounds on the mutual information between the input and the output sequences. For the deletion channel, we

insertion and deletion events (indels) in addition to base substitutions. The crux of the model is the treatment of indels as processes as opposed to the patterns implied by multiple sequence alignment. The results of this procedure are directly compatible with parsimony-based tree lengths. In addition

Insertions and deletions (indels) in a gene may cause severe genetic diseases, because translation of the gene often becomes frame-shifted. Indels frequently create a new stop codon which terminates the amino acid translation. Large Resequencing projects demand fully automated calls

Genomes Project hopes to sequence hundreds of human genotypes, but at low coverage (4-6x), and most of the current methods are unable to discover insertion/deletion and structural variants from this data. In order to identify indels from multiple low-coverage individuals we have developed the Mo

Double strand DNA breaks in plants are primarily repaired via non-homologous end joining. However, little is known about the molecular events underlying this process. We have studied non-homologous end joining of linearized plasmid DNA with different termini configurations following transformation

Alu repeats contribute to genomic instability in primates via insertional and recombinational mutagenesis. Here, we report an analysis of Alu elementinduced genomic instability through a novel mechanism termed retrotransposition-mediated deletion, and assess its impact on the integrity of primate