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The alignment or mapping of Deoxyribonucleic Acid (DNA) reads produced by the new massively parallel sequencing machines is a fundamental initial step in the DNA analysis process. DNA alignment consists of ordering millions of short nucleotide sequences called reads, using a previously sequenced genome as a reference, to reconstruct the genetic code of a species. Even with the efforts made in the development of new multi-stage alignment programs, based on sophisticated algorithms and new filtering heuristics, the execution times remain limiting for the development of various applications such as epigenetics and genomic medicine. This paper presents an overview of recent developments in the acceleration of DNA alignment programs, with special emphasis on those based on hardware, in particular Graphics Processing Units (GPUs), Field Programmable Gate Arrays (FPGAs), and Processing-in-Memory (PIM) devices. Unlike most of the works found in the literature, which review only the proposals that gradually emerged in some specific acceleration technology, this work analyzes the contemporary state of the subject in a more comprehensive way, covering from the conception of the problem, the modern sequencing technologies and the analysis of the structure of the new alignment programs, to the most innovative software and hardware acceleration techniques. The foregoing allows to clearly define, at the end of the paper, the trends, challenges and opportunities that still prevail in the field. We hope that this work will serve as a guide for the development of new and more sophisticated DNA alignment systems.

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This paper considers the problem of inferring an original sequence from a number of erroneous copies. The problem arises in DNA sequencing, particularly in the context of emerging technologies that provide high throughput or other advantages at the cost of an increased number of errors. We describe and compare two approaches that have recently been developed by the authors. The first approach searches for a sequence known as a Steiner string; the second searches for the most probable original sequence with respect to a simple Bayesian model of sequencing errors. We present the results of extensive tests in which erroneous copies of real DNA sequences were simulated and the algorithms were used to infer the original sequences. The results are used to compare the two approaches to each other and to a third, more conventional, approach based on multiple sequence alignment. We find that the Bayesian approach is superior to the Steiner approach, which in turn is superior to the alignment approach.

The two new algorithms can also be used to construct multiple sequence alignments. We show that the two methods produce alignments of approximately equal quality, and conclude that the Steiner approach is better for this purpose because it is faster. Both methods produce better alignments than a well-known multiple sequence alignment package, for the cases tested.

This article is about the research done in Bioinformatics Institute. It describes the research focus of the team at BII. It also summarizes the ongoing collaborations and partnerships the institution has with other partners.

The article is about Biopolis Shared Facilities. It is an overview of the purpose-built resource that provides research support to the Biopolis community. It mentions the facilities, equipment and technologies that it offers to the Biopolis community.

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We report an integrated nanochannel/nanoelectrode sensor for the detection of DNA using alternating currents. We find that DNA can be detected using platinum as the metal for the detecting electrodes, with a signal to noise ratio exceeding 10. We argue that the signal is at least in part electrochemical in nature, thus holds the promise to yield a sequence-dependent signal. However, we also find that for large voltages, DNA attaches irreversibly to the driving electrodes.

Nanopore-based devices are emerging as unique technique for fast and high-resolution detection of DNA bases. Recently, the two-dimensional (2D) materials have been identified as promising materials for nanopore devices due to its high sensitivity and label-free sensing of DNA bases. It is really challenging to transfer nanoscale film structure onto target substrates to fabricate nanopore devices of 2D materials. Herein, we report a mild and efficient transfer method based on the mediator of poly-propylene carbonate and elastic stamp. Through this method, most of the 2D materials are able to be transferred onto fragile substrates without hurting the substrate. Experimental observation shows that fabricated nanostructures adhere to the surface of substrates closely free of wrinkles and bubbles. Moreover, this method enables the fabrication of multilayered structures of complimentary 2D materials and offers the potential method to fabricate functionalized devices.