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https://www.readbyqxmd.com/read/28289437/best-hits-of-11110110111-model-free-selection-and-parameter-free-sensitivity-calculation-of-spaced-seeds
#1
Laurent Noé
BACKGROUND: Spaced seeds, also named gapped q-grams, gapped k-mers, spaced q-grams, have been proven to be more sensitive than contiguous seeds (contiguous q-grams, contiguous k-mers) in nucleic and amino-acid sequences analysis. Initially proposed to detect sequence similarities and to anchor sequence alignments, spaced seeds have more recently been applied in several alignment-free related methods. Unfortunately, spaced seeds need to be initially designed. This task is known to be time-consuming due to the number of spaced seed candidates...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28245816/string-kernels-for-protein-sequence-comparisons-improved-fold-recognition
#2
Saghi Nojoomi, Patrice Koehl
BACKGROUND: The amino acid sequence of a protein is the blueprint from which its structure and ultimately function can be derived. Therefore, sequence comparison methods remain essential for the determination of similarity between proteins. Traditional approaches for comparing two protein sequences begin with strings of letters (amino acids) that represent the sequences, before generating textual alignments between these strings and providing scores for each alignment. When the similitude between the two protein sequences to be compared is low however, the quality of the corresponding sequence alignment is usually poor, leading to poor performance for the recognition of similarity...
February 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28187069/virtual-modeling-of-postoperative-alignment-following-adult-spinal-deformity-asd-surgery-helps-predict-associations-between-compensatory-spinopelvic-alignment-changes-overcorrection-and-proximal-junctional-kyphosis-pjk
#3
Renaud Lafage, Shay Bess, Steve Glassman, Christopher Ames, Doug Burton, Robert Hart, Han Jo Kim, Eric Klineberg, Jensen Henry, Breton Line, Justin Scheer, Themistocles Protopsaltis, Frank Schwab, Virginie Lafage
STUDY DESIGN: Retrospective review of a prospective multicenter database. OBJECTIVE: To develop a method to analyze sagittal alignment, free of PJK's influence, and then compare PJK to non-PJK patients using this method. SUMMARY OF BACKGROUND DATA: Proximal Junctional Kyphosis (PJK) following Adult Spinal Deformity (ASD) surgery remains problematic as it alters sagittal alignment. This study proposes a novel virtual modeling technique that attempts to eliminate the confounding effects of PJK on postoperative spinal alignment...
February 9, 2017: Spine
https://www.readbyqxmd.com/read/28158113/light-splitting-with-imperfect-wave-plates
#4
Jarom S Jackson, James L Archibald, Dallin S Durfee
We discuss the use of wave plates with arbitrary retardances, in conjunction with a linear polarizer, to split linearly polarized light into two linearly polarized beams with an arbitrary splitting fraction. We show that for non-ideal wave plates, a much broader range of splitting ratios is typically possible when a pair of wave plates, rather than a single wave plate, is used. We discuss the maximum range of splitting fractions possible with one or two wave plates as a function of the wave plate retardances, and how to align the wave plates to achieve the maximum splitting range possible when simply rotating one of the wave plates while keeping the other one fixed...
February 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/28158040/simple-delay-limited-sideband-locking-with-heterodyne-readout
#5
Christoph Reinhardt, Tina Müller, Jack C Sankey
We present a robust sideband laser locking technique ideally suited for applications requiring low probe power and heterodyne readout. By feeding back to a high-bandwidth voltage-controlled oscillator, we lock a first-order phase-modulation sideband to a high-finesse Fabry-Perot cavity in ambient conditions, achieving a closed-loop bandwidth of 3.5 MHz (with a single integrator) limited fundamentally by the signal delay. The measured transfer function of the closed loop agrees with a simple model based on ideal system components, and from this we suggest a modified design that should achieve a bandwidth exceeding 6 MHz with a near-causally limited feedback gain as high as 4 × 10<sup>7</sup> at 1 kHz...
January 23, 2017: Optics Express
https://www.readbyqxmd.com/read/28157951/fano-resonances-in-cone-shaped-inwall-capillary-based-microsphere-resonator
#6
Xiaobei Zhang, Yong Yang, Haiyang Shao, Huawen Bai, Fufei Pang, Hai Xiao, Tingyun Wang
In this paper, we demonstrate a cone-shaped inwall coupler for excitation of the whispering-gallery modes (WGMs) of a microsphere resonator. The coupler is composed of a single mode fiber (SMF) and a capillary with an inner diameter of 5 μm. After immersing the capillary front end vertically into Hydrofluoric acid to obtain a cone inside the capillary, light in the SMF couples into the capillary efficiently while the hollow core is wide enough for a microsphere to be inserted. Because the front end face of the capillary acts as a reflector, a Fano resonance with an asymmetric line shape and a Q-factor of 2...
January 23, 2017: Optics Express
https://www.readbyqxmd.com/read/28154557/robust-inference-of-genetic-exchange-communities-from-microbial-genomes-using-tf-idf
#7
Yingnan Cong, Yao-Ban Chan, Charles A Phillips, Michael A Langston, Mark A Ragan
Bacteria and archaea can exchange genetic material across lineages through processes of lateral genetic transfer (LGT). Collectively, these exchange relationships can be modeled as a network and analyzed using concepts from graph theory. In particular, densely connected regions within an LGT network have been defined as genetic exchange communities (GECs). However, it has been problematic to construct networks in which edges solely represent LGT. Here we apply term frequency-inverse document frequency (TF-IDF), an alignment-free method originating from document analysis, to infer regions of lateral origin in bacterial genomes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28113331/alignment-free-self-calibrating-elbow-angles-measurement-using-inertial-sensors
#8
Philipp Muller, Marc-Andre Begin, Thomas Schauer, Thomas Seel
Due to their relative ease of handling and low cost, inertial measurement unit (IMU)-based joint angle measurements are used for a widespread range of applications. These include sports performance, gait analysis and rehabilitation (e.g. Parkinson's disease monitoring or post-stroke assessment). However, a major downside of current algorithms, recomposing human kinematics from IMU data, is that they require calibration motions and/or the careful alignment of the IMUs with respect to the body segments. In this article, we propose a new method, which is alignment-free and self-calibrating using arbitrary movements of the user and an initial zero reference arm pose...
December 14, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28109252/rna-tvcurve-a-web-server-for-rna-secondary-structure-comparison-based-on-a-multi-scale-similarity-of-its-triple-vector-curve-representation
#9
Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang, Qin Ma
BACKGROUND: RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis...
January 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#10
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097055/comprehensive-transcriptome-analysis-provides-new-insights-into-nutritional-strategies-and-phylogenetic-relationships-of-chrysophytes
#11
Daniela Beisser, Nadine Graupner, Christina Bock, Sabina Wodniok, Lars Grossmann, Matthijs Vos, Bernd Sures, Sven Rahmann, Jens Boenigk
BACKGROUND: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms...
2017: PeerJ
https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#12
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073754/fast-and-accurate-phylogeny-reconstruction-using-filtered-spaced-word-matches
#13
Chris-André Leimeister, Salma Sohrabi-Jahromi, Burkhard Morgenstern
MOTIVATION: Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. RESULTS: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28053114/feelnc-a-tool-for-long-non-coding-rna-annotation-and-its-application-to-the-dog-transcriptome
#14
Valentin Wucher, Fabrice Legeai, Benoît Hédan, Guillaume Rizk, Lætitia Lagoutte, Tosso Leeb, Vidhya Jagannathan, Edouard Cadieu, Audrey David, Hannes Lohi, Susanna Cirera, Merete Fredholm, Nadine Botherel, Peter A J Leegwater, Céline Le Béguec, Hille Fieten, Jeremy Johnson, Jessica Alföldi, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Thomas Derrien
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28008336/micado-looking-for-mutations-in-targeted-pacbio-cancer-data-an-alignment-free-method
#15
Justine Rudewicz, Hayssam Soueidan, Raluca Uricaru, Hervé Bonnefoi, Richard Iggo, Jonas Bergh, Macha Nikolski
Targeted sequencing is commonly used in clinical application of NGS technology since it enables generation of sufficient sequencing depth in the targeted genes of interest and thus ensures the best possible downstream analysis. This notwithstanding, the accurate discovery and annotation of disease causing mutations remains a challenging problem even in such favorable context. The difficulty is particularly salient in the case of third generation sequencing technology, such as PacBio. We present MICADo, a de Bruijn graph based method, implemented in python, that makes possible to distinguish between patient specific mutations and other alterations for targeted sequencing of a cohort of patients...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27992350/alignment-free-self-calibrating-elbow-angles-measurement-using-inertial-sensors
#16
Philipp Muller, Marc-Andre Begin, Thomas Schauer, Thomas Seel
Due to their relative ease of handling and low cost, inertial measurement unit (IMU)-based joint angle measurements are used for a widespread range of applications. These include sports performance, gait analysis and rehabilitation (e.g. Parkinson's disease monitoring or post-stroke assessment). However, a major downside of current algorithms, recomposing human kinematics from IMU data, is that they require calibration motions and/or the careful alignment of the IMUs with respect to the body segments. In this article, we propose a new method, which is alignment-free and self-calibrating using arbitrary movements of the user and an initial zero reference arm pose...
December 14, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/27992242/a-multiresolution-graphical-representation-for-similarity-relationship-and-multiresolution-clustering-for-biological-sequences
#17
Lianping Yang, Weilin Zhang
How we can describe the similarity relationship between the biological sequences is a basic but important problem in bioinformatics. The first graphical representation method for the similarity relationship rather than for single sequence is proposed in this article, which makes the similarity intuitional. Some properties such as sensitivity and continuity of the similarity are proved theoretically, which indicate that the similarity describer has the advantage of both alignment and alignment-free methods. With the aid of multiresolution analysis tools, we can exhibit the similarity's different profiles, from high resolution to low resolution...
December 19, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27977308/zika-and-flaviviruses-phylogeny-based-on-the-alignment-free-natural-vector-method
#18
Yongkun Li, Lily He, Rong Lucy He, Stephen S-T Yau
Zika virus (ZIKV) is a mosquito-borne flavivirus. It was first isolated from Uganda in 1947 and has become an emergent event since 2007. However, because of the inconsistency of alignment methods, the evolution of ZIKV remains poorly understood. In this study, we first use the complete protein and an alignment-free method to build a phylogenetic tree of 87 Zika strains in which Asian, East African, and West African lineages are characterized. We also use the NS5 protein to construct the genetic relationship among 44 Zika strains...
February 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/27924268/effects-of-the-difference-in-similarity-measures-on-the-comparison-of-ligand-binding-pockets-using-a-reduced-vector-representation-of-pockets
#19
Tsukasa Nakamura, Kentaro Tomii
Comprehensive analysis and comparison of protein ligand-binding pockets are important to predict the ligands which bind to parts of putative ligand binding pockets. Because of the recent increase of protein structure information, such analysis demands a fast and efficient method for comparing ligand binding pockets. Previously we proposed a fast alignment-free method based on a simple representation of a ligand binding pocket with one 11-dimensional vector, which is suitable for such analysis. Based on that method, we conducted this study to expand and revise similarity measures of binding pockets and to investigate the effects of those modifications with two datasets for improving the ability to detect similar binding pockets...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27918587/an-alignment-free-algorithm-in-comparing-the-similarity-of-protein-sequences-based-on-pseudo-markov-transition-probabilities-among-amino-acids
#20
Yushuang Li, Tian Song, Jiasheng Yang, Yi Zhang, Jialiang Yang
In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences...
2016: PloS One
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