We report the identification and characterization of 2,000 human diallelic insertion/deletion polymorphisms (indels) distributed throughout the human genome. Candidate indels were identified by comparison of overlapping genomic or cDNA sequences. Average confirmation rate for indels with a > or =2-nt allele-length difference was 58%, but the confirmation rate for indels with a 1-nt length diffe...

Short insertions and deletions (InDels) are one of the major genetic variants and are distributed widely across the genome; however, few investigations of InDels have been conducted in long-lived perennial plants. Here, we employed a combination of RNA-seq and population resequencing to identify InDels within differentially expressed (DE) genes underlying wood formation in a natural population ...

Insertion and deletion (indel) events usually have dramatic effects on genome structure and gene function. Species-specific indels have been demonstrated to be associated with species-unique traits. Currently, indel identifications mainly rely on pairwise sequence alignments (the ‘pair-wise indels’), which suffer lack of discrimination of species specificity and insertion versus deletion. Also,...

It was recently shown that indels are responsible for more than twice as many unmatched nucleotides as are base substitutions between samples of chimpanzee and human DNA. A larger sample has now been examined and the result is similar. The number of indels is approximately 1/12th of the number of base substitutions and the average length of the indels is 36 nt, including indels up to 10 kb. The...

Human-specific small insertions and deletions (HS indels, with lengths <100 bp) are reported to be ubiquitous in the human genome. However, whether these indels contribute to human-specific traits remains unclear. Here we employ a modified McDonald-Kreitman (MK) test and a combinatorial population genetics approach to infer, respectively, the occurrence of positive selection and recent selectiv...

Indel mutations play key roles in genome and protein evolution, yet we lack a comprehensive understanding of how indels impact evolutionary processes. Genome-wide analyses enabled by next-generation sequencing can clarify the context and effect of indels, thereby integrating a more detailed consideration of indels with our knowledge of nucleotide substitutions. To this end, we sequenced Blochma...

Insertion/deletion (indel) is one of the most common methods of protein sequence variation. Recent studies showed that indels could affect their flanking regions and they are important for protein function and evolution. Here, we describe the Indel Flanking Region Database (IndelFR, http://indel.bioinfo.sdu.edu.cn), which provides sequence and structure information about indels and their flanki...

In this review, we focus on progress that has been made with detecting small insertions and deletions (INDELs) in human genomes. Over the past decade, several million small INDELs have been discovered in human populations and personal genomes. The amount of genetic variation that is caused by these small INDELs is substantial. The number of INDELs in human genomes is second only to the number o...

Amino acid substitution and insertions/deletions (indels) are two common events in protein evolution; however, current knowledge on indels is limited. In this study, we investigated the effects of indels on the flanking regions in protein structure superfamilies. Comprehensive analysis of structural classification of proteins superfamilies revealed that indels lead to a series of changes in the...

MicroRNAs (miRNAs) are small noncoding RNA that play an important role in posttranscriptional regulation of mRNA. Genetic variations in miRNAs or their target sites have been shown to alter miRNA function and have been associated with risk for several diseases. Previous studies have focused on the most abundant type of genetic variations, single nucleotide polymorphisms (SNPs) that affect miRNA...