BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Improving co-development through process alignment

There has been a recent surge of enthusiasm icithin tlie automotive industry to build closer supplier relationships idthin the area of product development. One concept deemed central to these relationships is the alignment of development processes between the collaborating organizations, an area that is expanded upon idthin this paper. We suggest that synchronization can be achieved through the four key steps of process standardization, knowledge sliaring, alignment of existing practices, and continuous elimination oftcaste idthin the joint development cycles. A methodology for implementing these stages is presented along idth the underlying prindples on which it is based - the importance of joint teamworking and multi-company involvement idthin the alignment process is higlilighted. © MCB University Press.

Image sequence segmentation using mixture-models with uniqueness and spatio-temporal consistency constraints

The use of mixture-model techniques for motion estimation and image sequence segmentation was discussed. The issues such as modeling of occlusion and uncovering, determining the relative depth of the objects in a scene, and estimating the number of objects in a scene were also investigated. The segmentation algorithm was found to be computationally demanding, but the computational requirements were reduced as the motion parameters and segmentation of the frame were initialized. The method provided a stable description, in whichthe addition and removal of objects from the description corresponded to the entry and exit of objects from the scene.

XMolecular Cloning and Sequence Analyses of cDNAs Encoding Seven C2type Lectin2like Protein Subunits from Daboia russellii siamensis

按照Promega 公司的mRNA 提取试剂盒操作手册, 从圆斑蝰蛇( Daboia russellii siamensis ) 的毒腺中提 取mRNA ; 利用RT2PCR 的方法进行体外扩增, 获得C - 型凝集素蛋白的基因, 克隆到pMD182T 载体中。随机挑 选14 个阳性克隆进行核酸测序, 获得7 个编码不同蛇毒C - 型凝集素样蛋白亚基的cDNA , 分别命名为DRS2L1 、 DRS2L2 、DRS2L3 、DRS2L4 、DRS2L5 、DRS2L6 和DRS2L7 。由基因序列推导出的氨基酸序列表明, 克隆到的7 个蛇 毒C - 型凝集素样蛋白的亚基中均有糖识别结构域存在。BLAST 分析显示, 仅有DRS2L1 的蛋白序列与目前已知 的蛇毒C - 型凝集素样蛋白的α亚基相似。序列同源性比较并结合半胱氨酸位点分析, 推测DRS2L1 和DRS2L2 可能分别是圆斑蝰蛇毒Ⅹ因子激活剂的轻链LC2 和LC1 。DRS2L3 和DRS2L4 可能是高分子量的蛇毒C - 型凝集 素样蛋白的β亚基, 而DRS2L5 和DRS2L6 可能是低分子量的蛇毒C - 型凝集素样蛋白的β亚基。DRS2L7 可能是 类似于血小板膜糖蛋白Ib 结合蛋白的β亚基。

Statistical analysis of sequence features of introns with positive transcriptional regulation in yeast genes

A great deal of experimental studies have shown that many introns of eukaryotic genes function as regulators of transcription. However, comprehensive studies of this problem have not yet been conducted. After checking the transcription frequencies of some Saccharomyces cerevisiae (yeast), genes and their introns, a remarkable phenomenon was discovered that generally the introns of the genes with higher transcription frequencies are longer, and the introns of the genes with lower transcription frequencies are shorter. This suggests that the longer introns of genes with higher transcription frequencies may contain some characteristic sequence structures, which could enhance the transcription of genes. Therefore, two sets of introns of yeast genes were chosen for further study. The transcription frequencies of the first set of genes are higher (>30), and those of the second set of genes are lower (less than or equal to10). Some oligonucleotides are detected by statistically comparative analyses of the occurrence frequencies of oligonucleotides (mainly tetranucleotides and pentanucleotides), whose occurrence frequencies in the first set of introns; are significantly higher than those in the second set of introns, and are also significantly higher than those in the exons flanking the introns of the first set. Some of these extracted oligonucleotides are the same as the regulatory elements of transcription revealed by experimental analyses. Besides, the distributions of these extracted oligonucleotides in the two sets of introns and the exons show that the sequence structures of the first set of introns are favorable for transcription of genes.

Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome

We analyzed n-mers (n=3-8) in the local environment of 8,249,446 human SNPs and compared their distribution with that in the genome reference sequences. The results revealed that the short sequences, which contained at least one CpG dinucleotide, occurred

Sequence context analysis in the mouse genome: Single nucleotide polymorphisms and CpG island sequences

A genome-wide view of sequence mutability in mice is still limited, although biologists usually assume the same scenario for mice as for humans. In this study, we examined the sequence context in the local environment of 482,528 mouse single nucleotide po

Local synthesis and alignment of zinc oxide nanowires in aqueous solution using microheaters

A bottom-up technique for synthesizing transversely suspended zinc oxide nanowires (ZnO NWs) under a zinc nitrate (Zn(NO 3) 2· 6H 2O) and hexamethylenetetramine (HMTA, (CH 2) 6·N 4) solution within a microfabricated device is reported in this paper. The device consists of a microheater which is used to initially create an oxidized ZnO seed layer. ZnO NWs are then locally synthesized by the microheater and electrodes embedded within the devices are used to drive electric field directed horizontal alignment of the nanowires within the device. The entire process is carried out at low temperature. This approach has the potential to considerably simplify the fabrication and assembly of ZnO nanowires on CMOS compatible substrates, allowing for the chemical synthesis to be carried out under near-ambient conditions by locally defining the conditions for nanowire growth on a silicon reactor chip. © 2012 IEEE.

Statistics and dynamics of turbulence-flame alignment in premixed combustion

The geometric alignment of turbulent strain-rate structures with premixed flames greatly influences the results of the turbulence-flame interaction. Here, the statistics and dynamics of this alignment are experimentally investigated in turbulent premixed Bunsen flames using high-repetition-rate stereoscopic particle image velocimetry. In all cases, the statistics showed that the most extensive principal strain-rate associated with the turbulence preferentially aligned such that it was more perpendicular than parallel to the flame surface normal direction. The mean turbulence-flame alignment differed between the flames, with the stronger flames (higher laminar flame speed) exhibiting stronger preferential alignment. Furthermore, the preferential alignment was greatest on the reactant side of the mean flame brush. To understand these differences, individual structures of fluid-dynamic strain-rate were tracked through time in a Lagrangian manner (i.e., by following the fluid elements). It was found that the flame surface affected the orientation of the turbulence structures, with the majority of structures rotating as they approached the flame such that their most extensive principal strain-rate was perpendicular to the flame normal. The maximum change in turbulent structure orientation was found to decrease with the strength of the structure, increase with the strength of the flame, and exhibit similar trends when the structure strength and flame strength were represented by a Karlovitz number. The mean change in orientation decreased from the unburnt to burnt side of the flame brush and appears to be influenced by the overall flame shape. © 2011 The Combustion Institute.

Spontaneous induction of the uniform lying helix alignment in bimesogenic liquid crystals for the flexoelectro-optic effect

Using in-plane electric fields, the electrical induction of the uniform lying helix (ULH) alignment in chiral nematic liquid crystals is reported. This process permits spontaneous induction of the ULH alignment to give an in-plane optic axis, without the need for complex processing. Flexoelectro-optic switching is subsequently obtained by holding the in-plane electrodes at a common voltage and addressing via a third, plane-parallel electrode on a second, or upper, substrate to give a field across the device in the viewing direction. For this device, in optimized bimesogenic materials, we demonstrate full intensity modulation and sub-millisecond response times at typical device temperatures. © 2012 American Institute of Physics.

Low molar mass organosiloxane liquid crystals for telecommunication applications

Mixtures of two proprietary low molar mass organosiloxane liquid crystals were studied in order to improve their alignment and optimize their electro-optic properties for telecommunication applications. Over a certain concentration range, mixtures exhibited an isotropic-chiral smectic A-chiral smectic C (Iso-SmA*-SmC*) phase sequence leading to exceptionally good alignment. At room temperature, the spontaneous polarization of these samples was reduced from 225 nC cm -2 in the pure SmC* liquid crystal to as low as 75 nC cm -2 in the mixture. Within this concentration range, the ferroelectric tilt angle could be varied between 35° and 15°, while the rise time decreased by 69.4%. The rise times were < 45 μs for moderate electric fields of ± 10 V μm -1 in the SmC* phase and ∼ 4 μs, independent of electric field, in the SmA* phase. At λ = 1550 nm, these mixtures exhibited very large extinction ratios of {\sim} 60 dB for binary switching in the SmC* phase and ∼ 55 dB continuous variable attenuation in the SmA* phase. © 2012 IEEE.

Auto-calibration of a camera system using Image Alignment

Calibration of a camera system is a necessary step in any stereo metric process. It correlates all cameras to a common coordinate system by measuring the intrinsic and extrinsic parameters of each camera. Currently, manual calibration of a camera system is the only way to achieve calibration in civil engineering operations that require stereo metric processes (photogrammetry, videogrammetry, vision based asset tracking, etc). This type of calibration however is time-consuming and labor-intensive. Furthermore, in civil engineering operations, camera systems are exposed to open, busy sites. In these conditions, the position of presumably stationary cameras can easily be changed due to external factors such as wind, vibrations or due to an unintentional push/touch from personnel on site. In such cases manual calibration must be repeated. In order to address this issue, several self-calibration algorithms have been proposed. These algorithms use Projective Geometry, Absolute Conic and Kruppa Equations and variations of these to produce processes that achieve calibration. However, most of these methods do not consider all constraints of a camera system such as camera intrinsic constraints, scene constraints, camera motion or varying camera intrinsic properties. This paper presents a novel method that takes all constraints into consideration to auto-calibrate cameras using an image alignment algorithm originally meant for vision based tracking. In this method, image frames are taken from cameras. These frames are used to calculate the fundamental matrix that gives epipolar constraints. Intrinsic and extrinsic properties of cameras are acquired from this calculation. Test results are presented in this paper with recommendations for further improvement.