While indel rate variation has been observed and analyzed in detail, it is not taken into account by current indel-aware phylogenetic reconstruction methods. In this work, we introduce a continuous time stochastic process, the geometric Poisson indel process, that generalizes the Poisson indel process by allowing insertion and deletion rates to vary across sites. We design an efficient algorith...

It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred at the same position in two independent evolutionary lineages, and thus, indel-based inference of phylogeny should be less subject to homoplasy compared with standard inference which is based on substitution events. Indeed, indels were successfully used to solve debated evolutionary relationships ...

Flax is an important oil and fibre crop grown in Northern Europe, Canada, India, China. The development of molecular markers has accelerated the process flax breeding improved yield quality. Presently, simple sequence repeat (SSR) single nucleotide polymorphism (SNP) whole genome have been developed for flax. However, insertion/deletion (InDel) not reported. A total 17,110 InDel were identified...

This meta-analysis aimed to provide an up-to-date comprehensive evaluation on the association between the MDM2 40bp indel polymorphism and cancer susceptibility. Eligible studies were retrieved by searching Web of Science, PubMed, Scopus, and Google scholar databases up to August 27, 2018. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to estimate the ...

This meta-analysis aimed to provide an up-to-date comprehensive evaluation on the association between the MDM2 40bp indel polymorphism and cancer susceptibility. Eligible studies were retrieved by searching Web of Science, PubMed, Scopus, and Google scholar databases up to August 27, 2018. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to estimate the ...

Insertion and deletion (indel) mutations, the most common type of structural variance in the human genome, affect a multitude of human traits and diseases. New sequencing technologies, such as deep sequencing, allow massive throughput of sequence data and greatly contribute to the field of disease causing mutation detection, in general, and indel detection, specifically. In order to infer indel...

Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. ...

BACKGROUND At least two genetically different porcine epidemic diarrhea virus (PEDV) strains have been identified in the United States (U.S. PEDV prototype and S-INDEL-variant strains). The current serological assays offered at veterinary diagnostic laboratories for detection of PEDV-specific antibody are based on the U.S. PEDV prototype strain. The objectives of this study were: 1) isolate the...

It is increasingly recognized that insertions and deletions (indels) are an important source of genetic as well as phenotypic divergence and diversity. We analyzed length polymorphisms identified through partial (0.25x) shotgun sequencing of three breeds of domestic chicken made by the International Chicken Polymorphism Map Consortium. A data set of 140,484 short indel polymorphisms in unique D...