Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and ...

MOTIVATION Accurately predicting and genotyping indels longer than 30 bp has remained a central challenge in next-generation sequencing (NGS) studies. While indels of up to 30 bp are reliably processed by standard read aligners and the Genome Analysis Toolkit (GATK), longer indels have still resisted proper treatment. Also, discovering and genotyping longer indels has become particularly releva...

Backbone modifications via insertions and deletions (InDels) may exert dramatic effects, for better (mediating new functions) and for worse (causing loss of structure and/or function). However, contrary to point mutations (substitutions), our knowledge of the evolution and structural-functional effects of InDels is limited and so is our capability to engineer them. We sought to assess how delet...

Indels in the coding regions of a gene can either cause frameshifts or amino acid insertions/deletions. Frameshifting indels are indels that have a length that is not divisible by 3 and subsequently cause frameshifts. Indels that have a length divisible by 3 cause amino acid insertions/deletions or block substitutions; we call these 3n indels. The new amino acid changes resulting from 3n indels...

Small insertions/deletions (INDELs) of ≤21 bp comprise 18% of all recorded mutations causing human inherited disease and are evident in 24% of documented Mendelian diseases. INDELs affect gene function in multiple ways: for example, by introducing premature stop codons that either lead to the production of truncated proteins or affect transcriptional efficiency. However, the means by which they...

A molecular marker is a valuable tool in genetic research. Insertions–deletions (InDels) are commonly used polymorphisms gene mapping, analysing diversity, marker-assisted breeding, and phylogenetics. The 3000 Rice Genome Project, re-sequencing project, discovered millions of genome-wide InDels. We found that the proportion >50-bp long InDels (699,475) total (1,248,503) 56.02%. number on eac...

Short insertions and deletions (InDels) comprise an important part of the natural mutational repertoire. InDels are, however, highly deleterious, primarily because two-thirds result in frame-shifts. Bypass through slippage over homonucleotide repeats by transcriptional and/or translational infidelity is known to occur sporadically. However, the overall frequency of bypass and its relation to se...