Relevant bibliographies by topics / Accurate Alignment of Short Reads

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Academic literature on the topic 'Accurate Alignment of Short Reads'

Author: Grafiati
Published: 6 September 2023
Last updated: 31 July 2025

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Journal articles on the topic "Accurate Alignment of Short Reads"

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Carter, John Lawrence, Harlan Stevens, Perry G. Ridge, and Steven Michael Johnson. "Short Sequence Aligner Benchmarking for Chromatin Research." International Journal of Molecular Sciences 24, no. 18 (2023): 14074. http://dx.doi.org/10.3390/ijms241814074.

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Much of today’s molecular science revolves around next-generation sequencing. Frequently, the first step in analyzing such data is aligning sequencing reads to a reference genome. This step is often taken for granted, but any analysis downstream of the alignment will be affected by the aligner’s ability to correctly map sequences. In most cases, for research into chromatin structure and nucleosome positioning, ATAC-seq, ChIP-seq, and MNase-seq experiments use short read lengths. How well aligners manage these reads is critical. Most aligner programs will output mapped reads and unmapped reads.
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Asghari, Hossein, Yen-Yi Lin, Yang Xu, Ehsan Haghshenas, Colin C. Collins, and Faraz Hach. "CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme." Bioinformatics 36, no. 12 (2020): 3703–11. http://dx.doi.org/10.1093/bioinformatics/btaa232.

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Abstract Motivation The ubiquitous abundance of circular RNAs (circRNAs) has been revealed by performing high-throughput sequencing in a variety of eukaryotes. circRNAs are related to some diseases, such as cancer in which they act as oncogenes or tumor-suppressors and, therefore, have the potential to be used as biomarkers or therapeutic targets. Accurate and rapid detection of circRNAs from short reads remains computationally challenging. This is due to the fact that identifying chimeric reads, which is essential for finding back-splice junctions, is a complex process. The sensitivity of dis
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Mkrtchian, A. A., K. S. Grammatikati, P. G. Kazakova, et al. "Comparative Analysis of Structural Variant Callers on the Short-Read Whole-Genome Sequencing Data." Генетика 59, no. 6 (2023): 687–707. http://dx.doi.org/10.31857/s0016675823060115.

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In this study three structural variant callers (Manta, Smoove, Delly) were analysed on the whole-genome sequencing data using four different alignment algorithms: DRAGEN, GDC DNA-Seq Alignment Workflow, GDC DNA-Seq Alignment Workflow + GDC DNA-Seq Co-Cleaning Workflow, NovoAlign, different lengths of raw reads: 2 × 150 bp and 2 × 250 bp, different mean genome coverage values. Results were compared to etalon results of GIAB team. Structural variants validation was hold also with Sanger sequencing. Structural variants deletions and insertions as it turned out were best determined with Manta tool
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Kumar, Sanjeev, Suneeta Agarwal, and Ranvijay. "Fast and memory efficient approach for mapping NGS reads to a reference genome." Journal of Bioinformatics and Computational Biology 17, no. 02 (2019): 1950008. http://dx.doi.org/10.1142/s0219720019500082.

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New generation sequencing machines: Illumina and Solexa can generate millions of short reads from a given genome sequence on a single run. Alignment of these reads to a reference genome is a core step in Next-generation sequencing data analysis such as genetic variation and genome re-sequencing etc. Therefore there is a need of a new approach, efficient with respect to memory as well as time to align these enormous reads with the reference genome. Existing techniques such as MAQ, Bowtie, BWA, BWBBLE, Subread, Kart, and Minimap2 require huge memory for whole reference genome indexing and reads
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Flouri, Tomas, Costas S. Iliopoulos, Solon P. Pissis, and German Tischler. "Mapping Short Reads to a Genomic Sequence with Circular Structure." International Journal of Systems Biology and Biomedical Technologies 1, no. 1 (2012): 26–34. http://dx.doi.org/10.4018/ijsbbt.2012010103.

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Constant advances in DNA sequencing technologies are turning whole-genome sequencing into a routine procedure, resulting in massive amounts of data that need to be processed. Tens of gigabytes of data, in the form of short sequences (reads), need to be mapped back onto reference sequences, a few gigabases long. A first generation of short-read alignment algorithms successfully employed hash tables, and the current second generation uses the Burrows-Wheeler transform, further improving speed and memory footprint. These next-generation sequencing technologies allow researchers to characterise a
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Teixeira, Andreia Sofia, Francisco Fernandes, and Alexandre P. Francisco. "SpliceTAPyR — An Efficient Method for Transcriptome Alignment." International Journal of Foundations of Computer Science 29, no. 08 (2018): 1297–310. http://dx.doi.org/10.1142/s0129054118430049.

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RNA-Seq is a Next-Generation Sequencing (NGS) protocol for sequencing the messenger RNA in a cell and generates millions of short sequence fragments, reads, in a single run. These reads can be used to measure levels of gene expression and to identify novel splice variants of genes. One of the critical steps in an RNA-Seq experiment is mapping NGS reads to the reference genome. Because RNA-Seq reads can span over more than one exon in the genome, this task is challenging. In the last decade, tools for RNA-Seq alignment have emerged, but most of them run in two phases. First, the pipeline only m
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Ebler, Jana, Peter Ebert, Wayne E. Clarke, et al. "Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes." Nature Genetics 54, no. 4 (2022): 518–25. http://dx.doi.org/10.1038/s41588-022-01043-w.

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AbstractTypical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions, which are particularly challenging for fast k-mer-based genotypers. In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation—a pr
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Li, H., and R. Durbin. "Fast and accurate short read alignment with Burrows-Wheeler transform." Bioinformatics 25, no. 14 (2009): 1754–60. http://dx.doi.org/10.1093/bioinformatics/btp324.

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MAURER-STROH, SEBASTIAN, VITHIAGARAN GUNALAN, WING-CHEONG WONG, and FRANK EISENHABER. "A SIMPLE SHORTCUT TO UNSUPERVISED ALIGNMENT-FREE PHYLOGENETIC GENOME GROUPINGS, EVEN FROM UNASSEMBLED SEQUENCING READS." Journal of Bioinformatics and Computational Biology 11, no. 06 (2013): 1343005. http://dx.doi.org/10.1142/s0219720013430051.

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We propose an extension to alignment-free approaches that can produce reasonably accurate phylogenetic groupings starting from unaligned genomes, for example, as fast as 1 min on a standard desktop computer for 25 bacterial genomes. A 6-fold speed-up and 11-fold reduction in memory requirements compared to previous alignment-free methods is achieved by reducing the comparison space to a representative sample of k-mers of optimal length and with specific tag motifs. This approach was applied to the test case of fitting the enterohemorrhagic O104:H4 E.coli strain from the 2011 outbreak in German
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Ghoneimy, Samy, and Samir Abou El-Seoud. "A MapReduce Framework for DNA Sequencing Data Processing." International Journal of Recent Contributions from Engineering, Science & IT (iJES) 4, no. 4 (2016): 11. http://dx.doi.org/10.3991/ijes.v4i4.6537.

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<p class="Els-1storder-head">Genomics and Next Generation Sequencers (NGS) like Illumina Hiseq produce data in the order of ‎‎200 billion base pairs in a single one-week run for a 60x human genome coverage, which ‎requires modern high-throughput experimental technologies that can ‎only be tackled with high performance computing (HPC) and specialized software algorithms called ‎‎“short read aligners”. This paper focuses on the implementation of the DNA sequencing as a set of MapReduce programs that will accept a DNA data set as a FASTQ file and finally generate a VCF (variant call format)
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Dissertations / Theses on the topic "Accurate Alignment of Short Reads"

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Shajii, Ariya. "Fast and accurate alignment of barcoded reads." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118040.

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Thesis: S.M., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references (pages 57-62).<br>Over the last few years, we have seen the emergence of several so-called "third-generation" sequencing platforms, which improve on standard short-read sequencing that has thus far been at the center of next-generation sequencing. While technologies developed by Pacific Biosciences and Oxford Nanopore accomplish this goal by producing physically longer reads, several other technolog
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Porter, Jacob Stuart. "Mapping Bisulfite-Treated Short DNA Reads." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/82870.

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Epigenetics are stable heritable traits that are not a result of the DNA sequence. Epigenetic modification of DNA cytosine plays a role in development and disease. The covalent bonding of a methyl group or a hydroxymethyl group to the 5-carbon of cytosine epigenetically modifies cytosine to 5-methylcytosine or 5-hydroxymethylcytosine. Upon PCR amplification, the bisulfite treatment of DNA converts unmethylated cytosine to thymine, while 5-methylcytosine, 5-hydroxymethylcytosine, and other bases remain unchanged. The resulting sequences can be mapped to a reference genome; however, this can
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Berger, Simon A. [Verfasser], and A. [Akademischer Betreuer] Stamatakis. "Phylogeny-Aware Placement and Alignment Methods for Short Reads / Simon A. Berger. Betreuer: A. Stamatakis." Karlsruhe : KIT-Bibliothek, 2013. http://d-nb.info/1032243139/34.

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Tran, Hong Thi Thanh. "Evaluating and Improving Performance of Bisulfite Short Reads Alignment and the Identification of Differentially Methylated Sites." Diss., Virginia Tech, 2018. http://hdl.handle.net/10919/81861.

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Large-scale bisulfite treatment and short reads sequencing technology allows comprehensive estimation of methylation states of Cs in the genomes of different tissues, cell types, and developmental stages. Accurate characterization of DNA methylation is essential for understanding genotype phenotype association, gene and environment interaction, diseases, and cancer. The thesis work first evaluates the performance of several commonly used bisulfite short read mappers and investigates how pre-processing data might affect the performance. Aligning bisulfite short reads to a reference genome remai
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Natarajan, Santhi. "Accelerated and Accurate Alignment of Short Reads in High Throughput Next Generation Sequencing [NGS] Platforms." Thesis, 2016. http://etd.iisc.ac.in/handle/2005/4073.

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The genome of an organism encompasses the unique set of genetic instructions for every individual in a species. The genome, in totality, guides the course of evolution, development, genetic and epigenetic growth factors of an individual. Genomics, the study of genome, presents an interdisciplinary landscape, with a multistage data analytics pipeline. Understanding the genome involves determining the order of the four constituent nucleotides or bases or genetic alphabets, namely adenine (A), cytosine (C), guanine (G) and thymine (T), within the genome’s DNA sequence, and the process is widely k
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Lee, Sheng Ta, and 李昇達. "Develop RNA short reads alignment tool based on GPU with CUDA." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/22829209401562854641.

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碩士<br>長庚大學<br>資訊工程學系<br>100<br>After the reference genomes of many organisms are sequenced in the post-genetic era, an important issue is to do the re-sequencing of individual genomes with high-throughput reads. Many next-generation sequencing machines have been proposed in the last few years and a series of re-sequencing tools have been developed for mapping short reads to the reference genome. FRESCO is a frequency-based re-sequencing tool without using hash look-up table algorithm and Burrows Wheeler Transformation. FRESCO offers more flexibility in the mapping and then obtains satisfied ma
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Book chapters on the topic "Accurate Alignment of Short Reads"

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CLEMENTE, JOSÉ C., JESPER JANSSON, and GABRIEL VALIENTE. "ACCURATE TAXONOMIC ASSIGNMENT OF SHORT PYROSEQUENCING READS." In Biocomputing 2010. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789814295291_0002.

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"A Short Reads Alignment Algorithm Oriented to Massive Data." In Current Trends in Computer Science and Mechanical Automation Vol.1. De Gruyter Open Poland, 2017. http://dx.doi.org/10.1515/9783110584974-008.

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Tait, Roger, and Gerald Schaefer. "Distributed Medical Volume Registration." In Handbook of Research on Distributed Medical Informatics and E-Health. IGI Global, 2009. http://dx.doi.org/10.4018/978-1-60566-002-8.ch012.

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The registration of corresponding patient volumes is often a pre-requisite for medical imaging tasks. Accurate alignment, however, usually results in high computational complexity and can hence take a considerable amount of time. This is particularly true with 3-D volume data which adds another dimension to the registration process. One possibility of keeping registration times feasible is to distribute computation among several processors so that it maybe accomplished in parallel. This chapter provides a short survey of parallel registration approaches which have been proposed together with s
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D. Magar, Nakul, Priya Shah, K. Harish, et al. "Gene Expression and Transcriptome Sequencing: Basics, Analysis, Advances." In Gene Expression [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.105929.

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Gene expression studies are extremely useful for understanding a broad range of biological, physiological, and molecular responses. The techniques for gene expression reflect differential patterns of gene regulation and have evolved with time from detecting one gene to many genes at a time laterally. Gene expression depends on the spatiotemporal expression in a particular tissue at a given time point and needs critical examination and interpretation. Transcriptome sequencing or RNA-seq using next-generation sequencing (short and long reads) is the most widely deployed technology for accurate q
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Dhanush, P. S., Anil Chandra Adamane Ramesh, T. K. Nikhil Vyas, Anuradha Nayak Majila, Chandru D. Fernando, and S. Seetharamu. "Critical Parameters Influencing High-Strain Rate Deformation of Materials Using the Split-Hopkinson Pressure Bar Apparatus: A Review." In Advanced Materials for Emerging Applications (Innovations, Improvements, Inclusion and Impact). BENTHAM SCIENCE PUBLISHERS, 2024. http://dx.doi.org/10.2174/9789815196771124010020.

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Strength and ductility of materials at high strain rate of deformation are important for design engineers working in a wide range of industries, especially in gas turbine engine blades. Split Hopkinson pressure bar (SHPB) apparatus is a popular method of characterizing the high strain rate behaviour of materials. The results from the split-Hokinson pressure bar tests are further used in mathematical models such as Johnson-Cook model, Zerelli - Armstrong model and so on for correlation purposes. Split-Hopkinson pressure bar tests take place in a very short duration of time (less than a second)
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Conference papers on the topic "Accurate Alignment of Short Reads"

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Natarajan, Santhi, N. Krishna Kumar, Debnath Pal, and S. K. Nandy. "AccuRA: Accurate alignment of short reads on scalable reconfigurable accelerators." In 2016 International Conference on Embedded Computer Systems: Architectures, Modeling and Simulation (SAMOS). IEEE, 2016. http://dx.doi.org/10.1109/samos.2016.7818334.

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Cui, Xingchen, Hongzhi Shi, Jian Zhao, Yuan Ge, Yunfeng Yin, and Kun Zhao. "High Accuracy Short Reads Alignment Using Multiple Hash Index Tables on FPGA Platform." In 2020 IEEE 5th Information Technology and Mechatronics Engineering Conference (ITOEC). IEEE, 2020. http://dx.doi.org/10.1109/itoec49072.2020.9141738.

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Bingol, Zulal, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, and Can Alkan. "GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping." In 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2021. http://dx.doi.org/10.1109/ipdpsw52791.2021.00039.

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Lu, Zhi-Yuan, Jian-Ming Xie, and Xiao Sun. "Umap: Use Unique Sequence for Alignment of Short Sequence Reads and SNP Detection." In 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE). IEEE, 2010. http://dx.doi.org/10.1109/icbbe.2010.5516449.

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Yang, Yongjie, Cheng Zhong, and Danyang Chen. "Accelerating Alignment for Short Reads Allowing Insertion of Gaps on Multi-Core Cluster." In 2019 20th International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT). IEEE, 2019. http://dx.doi.org/10.1109/pdcat46702.2019.00019.

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Mahfoz, M. Y., A. K. Halim, A. H. A. Razak, M. F. Md Idros, F. N. Osman, and S. A. M. Al Junid. "Design and Analysis of Rotator Core for Short Reads Sequence Alignment Using Burrows-Wheeler Algorithm." In 2023 IEEE International Conference on Applied Electronics and Engineering (ICAEE). IEEE, 2023. http://dx.doi.org/10.1109/icaee58583.2023.10331049.

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Matoorian, R., M. Malaieri, R. Shor, and R. Aguilera. "Introducing a New Hybrid Data-Physics Architecture for Production Forecasting in Unconventional Wells." In SPE Canadian Energy Technology Conference and Exhibition. SPE, 2024. http://dx.doi.org/10.2118/218111-ms.

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Abstract This research presents a new architecture and implementation to overcome inherent challenges in leveraging machine learning (ML) for evaluating production performance in unconventional wells. By implementing a hybrid data-physics architecture (HDP), our goal is to effectively address several persistent hurdles, including generalizability limitations across diverse samples, the necessity for extensive training datasets, and the discrepancies between model predictions and fundamental physical principles. These fundamental constraints form the focal points of our comprehensive investigat
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Matsumoto, Shuichi, Hisaaki Arai, and Tomohiko Sakai. "Study of re-entry guidance for orbital recovery and rocket first stage recovery." In ESA 12th International Conference on Guidance Navigation and Control and 9th International Conference on Astrodynamics Tools and Techniques. ESA, 2023. http://dx.doi.org/10.5270/esa-gnc-icatt-2023-204.

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For new space transport missions such as orbital recovery from Low Earth Orbit (LEO) and the rocket first stage recovery, accurate reentry guidance has become increasingly important. JAXA realized two orbital recovery missions, Orbital Reentry Experiment (OREX) and HTV Small Re-entry Capsule (HSRC). The recovery accuracy of OREX is about 100km and those of HSRC is about 10km. However practical capsule recovery system will need about 1km accuracy to land on Japan mainland. In this paper shows the way to realize 1km reentry guidance accuracy, on-orbit alignment, IMU-Drag Measurement-GNSS navigat
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Nickol, Jeremy B., Randall M. Mathison, Michael G. Dunn, Jong S. Liu, and Malak F. Malak. "Unsteady Heat Transfer and Pressure Measurements on the Airfoils of a Rotating Transonic Turbine With Multiple Cooling Configurations." In ASME Turbo Expo 2016: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/gt2016-57768.

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Measurements are presented for a high-pressure transonic turbine stage operating at design-corrected conditions with forward and aft purge flow and blade film cooling in a short-duration blow-down facility. Four different film-cooling configurations are investigated: simple cylindrical-shaped holes, diffusing fan-shaped holes, an advanced-shaped hole, and uncooled blades. A rainbow turbine approach is used so each of the four blade types comprise a wedge of the overall bladed disk and are investigated simultaneously at identical speed and vane exit conditions. Double-sided Kapton heat-flux gau
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Flory, Alan P., and William C. Livoti. "The Effect and Remedy of Nozzle Loads on Boiler Feed Pumps." In ASME 2004 Power Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/power2004-52157.

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Many frequently encountered start-up and operational problems in current design combined cycle power plants can be traced to pipe strain and nozzle loads placed upon pumps. This is most dramatic when the boiler feed pump is affected. Many of the symptoms are significant and can include misalignment, dynamic (changing) alignment, pump or motor vibration, bearing problems, mechanical seal failures and seizure of equipment on start-up and shutdown. While these are all nuisance items that can plague plant shake-down and commissioning, some can generate huge costs and plant unscheduled outages. Mor
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Reports on the topic "Accurate Alignment of Short Reads"

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Steffenson, B. J., I. Mayrose, Gary J. Muehlbauer, and A. Sharon. ing and comparative sequence analysis of powdery mildew and leaf rust resistance gene complements in wild barley. United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134173.bard.

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Our overall, long-term goal is to exploit the genetic diversity present in cereal wild relatives for the development of cultivars with durable disease resistance. Our specific objectives for this proposal were to: 1) Utilize Association Genetics Resistance Gene Enrichment Sequencing (AgRenSeq) to identify and clone powdery mildew and leaf rust resistance gene complements in wild barley and 2) Conduct comparative sequence analyses of the cloned resistance genes to elucidate the basis of their specificity and evolution. The deployment of resistant cultivars is the most effective, economically ef
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