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https://www.readbyqxmd.com/read/28430779/a-coevolution-analysis-for-identifying-protein-protein-interactions-by-fourier-transform
#1
Changchuan Yin, Stephen S-T Yau
Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferring PPIs from protein sequences based on coevolution theory avoid these problems. In the coevolution theory model, interacted proteins may show coevolutionary mutations and have similar phylogenetic trees...
2017: PloS One
https://www.readbyqxmd.com/read/28422050/k-mer-content-correlation-and-position-analysis-of-genome-dna-sequences-for-the-identification-of-function-and-evolutionary-features
#2
Aaron Sievers, Katharina Bosiek, Marc Bisch, Chris Dreessen, Jascha Riedel, Patrick Froß, Michael Hausmann, Georg Hildenbrand
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used...
April 19, 2017: Genes
https://www.readbyqxmd.com/read/28369524/ngscheckmate-software-for-validating-sample-identity-in-next-generation-sequencing-studies-within-and-across-data-types
#3
Sejoon Lee, Soohyun Lee, Scott Ouellette, Woong-Yang Park, Eunjung A Lee, Peter J Park
In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files...
March 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28369270/dltree-efficient-and-accurate-phylogeny-reconstruction-using-the-dynamical-language-method
#4
Qi Wu, Zu-Guo Yu, Jianyi Yang
Summary: A number of alignment-free methods have been proposed for phylogeny reconstruction over the past two decades. But there are some long-standing challenges in these methods, including requirement of huge computer memory and CPU time, and existence of duplicate computations. In this article, we address these challenges with the idea of compressed vector, fingerprint and scalable memory management. With these ideas we developed the DLTree algorithm for efficient implementation of the dynamical language model and whole genome-based phylogenetic analysis...
March 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28362738/self-eclipsing-alignment-free-vortex-coronagraphy
#5
Artur Aleksanyan, Etienne Brasselet
We report on a self-induced strategy to achieve high-contrast optical imaging, without the need for any man-made optical masks, which relies on the self-induced spin-to-orbital angular momentum conversion phenomenon. This is experimentally demonstrated by realizing a laboratory demonstration of self-eclipsing of a light source following the generation of a self-adapted vectorial optical vortex transmission mask. The proposed concept, namely the realization of an alignment-free optical vortex coronagraph, may inspire the development of future generations of smart astronomical imaging instruments...
April 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28350835/an-information-based-network-approach-for-protein-classification
#6
Xiaogeng Wan, Xin Zhao, Stephen S T Yau
Protein classification is one of the critical problems in bioinformatics. Early studies used geometric distances and polygenetic-tree to classify proteins. These methods use binary trees to present protein classification. In this paper, we propose a new protein classification method, whereby theories of information and networks are used to classify the multivariate relationships of proteins. In this study, protein universe is modeled as an undirected network, where proteins are classified according to their connections...
2017: PloS One
https://www.readbyqxmd.com/read/28345370/an-accurate-and-fast-alignment-free-method-for-profiling-microbial-communities
#7
Diem-Trang Pham, Shanshan Gao, Vinhthuy Phan
Determining abundances of microbial genomes in metagenomic samples is an important problem in analyzing metagenomic data. Although homology-based methods are popular, they have shown to be computationally expensive due to the alignment of tens of millions of reads from metagenomic samples to reference genomes of hundreds to thousands of environmental microbial species. We introduce an efficient alignment-free approach to estimate abundances of microbial genomes in metagenomic samples. The approach is based on solving linear and quadratic programs, which are represented by genome-specific markers (GSM)...
March 7, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28289437/best-hits-of-11110110111-model-free-selection-and-parameter-free-sensitivity-calculation-of-spaced-seeds
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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...
April 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073754/fast-and-accurate-phylogeny-reconstruction-using-filtered-spaced-word-matches
#20
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...
April 1, 2017: Bioinformatics
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