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