Insertions and deletions in a genome.
1Short read aligners are well suited to single nucleotide and indel detection.
2SpartaABC implements an approximate-Bayesian-computation rejection algorithm to infer indel parameters from sequence data.
3The median numbers of somatic and indel mutations in MSI tumors were higher.
4It then performs numerous sequence simulations under randomly sampled indel parameters.
5The sequence of the indel, when present, was similar in the 12 isolates examined.
6As output, SpartaABC provides point estimates and approximate posterior distributions of the indel parameters.
7We then determined that the presence of the indel reduced transcriptional activity by half.
8Further, we evaluated the effects of sequencing coverage and indel misalignment on genotyping accuracy.
9Second, SpartaABC samples indel parameters from a prior distribution and uses them to simulate sequences.
10The previous indel reversion mutations were no longer detected.
11Using SpartaABC we demonstrate the differences in indel dynamics among three protein-coding genes across mammalian orthologs.
12Genotyping of the indel loci was performed by fragment length analysis after PCR and DNA sequencing.
13These results indicate that the GIGYF2 indel may be associated with increased risk of PD in northern China.
14A correlation was also demonstrated between the absence of the indel and the expression of the Hco-acr-8b transcript.
15Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA.
16We study the performance of our methodology and show that it provides accurate estimates of indel parameters in simulations.