Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA structure. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a uni...

AIMS To detect clonal T cell populations by high resolution polymerase chain reaction (PCR) using fluorescently labelled nucleotides and analysis on an ABI 377 DNA sequencer, and to evaluate this method using low ionic strength single strand conformation polymorphism (LIS-SSCP) analysis. METHODS DNA samples from 11 patients diagnosed with a T cell disease and 15 with no known T cell disorder ...

in india, holstein and its crosses are being used extensively in breeding programmes and all these breeding bulls are screened for autosomal recessive genes. blood samples are collected in ethylenediaminetetraacetic acid (edta) coated tubes and dna was isolated by using phenol-chloroform method. polymerase chain reaction restriction fragment length polymorphism (pcr-rflp) wereperformed by using...

BACKGROUND Cap analysis of gene expression (CAGE) is a 5' sequence tag technology to globally determine transcriptional starting sites in the genome and their expression levels and has most recently been adapted to the HeliScope single molecule sequencer. Despite significant simplifications in the CAGE protocol, it has until now been a labour intensive protocol. METHODOLOGY In this study we s...

High-throughput fluorescent genotyping requires a considerable amount of automation for accurate and efficient processing of genetic markers. Automated DNA sequencers and corresponding software products are commercially available that contribute substantially to increased throughput rates for large-scale genotyping projects. However, some conceptually simple tasks still require time-consuming m...

BACKGROUND: Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is performed mainly in patients with high-risk or advanced hematologic malignancies and congenital or acquired aplastic anemias. In the context of the significant risk of graft failure after allo-HSCT from alternative donors and the risk of relapse in recipients transplanted for malignancy, the precise monitoring of post...

Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon w...

Human tumor samples were screened for point mutations by adapting a mobility-shift assay to automated DNA sizing. This screen identifies the type of point mutation and relative amount of mutated DNA sequences present in a sample. Test samples having known hypoxanthine-guanine phosphoribosyl transferase (hprt)/exon-3 sequence mutations were characterized by: (i) PCR amplification, (ii) fluoresce...

New DNA sequencing technology implemented in the GS 20 sequencer reduces cost and time in exchange for lower accuracy. DNA sequencing errors negatively impact downstream applications and therefore accurate base calls and error probabilities are invaluable to researchers. This paper applies a graphical model to the base calling problem in context of the GS 20 sequencer. This model integrates sig...

This paper introduces a powerful novel sequencer for controlling computational machines and for structured DMA (direct memory access) applications. It is mainly focused on applications using 2-dimensional memory organization, where most inherent speed-up is obtained thereof. A classification scheme of computational sequencing patterns and storage schemes is derived. In the context of applicatio...