Ligase-based detection of mononucleotide repeat sequences

Ligase-based detection of mononucleotide repeat sequences.

Up to 15% of all colorectal cancers are considered to be replication error positive (RER(+)) and contain mutations at hundreds of thousands of microsatellite repeat sequences. Recently, a number of intragenic mononucleotide repeat sequences have been demonstrated to be targets for inactivating genes in RER(+)colorectal tumors. In this study, thermostable DNA ligases were tested for the ability ...

PCR amplification introduces errors into mononucleotide and dinucleotide repeat sequences.

The polymerase chain reaction (PCR) is used universally for accurate exponential amplification of DNA. We describe a high error rate at mononucleotide and dinucleotide repeat sequence motifs. Subcloning of PCR products allowed sequence analysis of individual DNA molecules from the product pool and revealed that: (1) monothymidine repeats longer than 11 bp are amplified with decreasing accuracy,...

Spectrum-Based De Novo Repeat Detection in Genomic Sequences

A novel approach to the detection of genomic repeats is presented in this paper. The technique, dubbed SAGRI (Spectrum Assisted Genomic Repeat Identifier), is based on the spectrum (set of sequence k-mers, for some k) of the genomic sequence. Specifically, the genome is scanned twice. The first scan (FindHit) detects candidate pairs of repeat-segments, by effectively reconstructing portions of ...

RepMaestro: scalable repeat detection on disk-based genome sequences

MOTIVATION We investigate the problem of exact repeat detection on large genomic sequences. Most existing approaches based on suffix trees and suffix arrays (SAs) are limited either to small sequences or those that are memory resident. We introduce RepMaestro, a software that adapts existing in-memory-enhanced SA algorithms to enable them to scale efficiently to large sequences that are disk re...

Detection of recombination in variable number tandem repeat sequences