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Nikolaj Kofoed Mandsberg, Ole Hansen, Rafael Taboryski
Droplet array chips were realized using an alignment-free fabrication process in silicon. The chips were textured with a homogeneous nano-scale surface roughness but were partially covered with a self-assembled monolayer of perfluorodecyltrichlorosilane (FDTS), resulting in a super-biphilic surface. When submerged in water and withdrawn again, microliter sized droplets are formed due to pinning of water on the hydrophilic spots. The entrained droplet volumes were investigated under variation of spot size and withdrawal velocity...
October 6, 2017: Scientific Reports
Xin Bai, Kujin Tang, Jie Ren, Michael Waterman, Fengzhu Sun
BACKGROUND: Alignment-free sequence comparison using counts of word patterns (grams, k-tuples) has become an active research topic due to the large amount of sequence data from the new sequencing technologies. Genome sequences are frequently modelled by Markov chains and the likelihood ratio test or the corresponding approximate χ (2)-statistic has been suggested to compare two sequences. However, it is not known how to best choose the word length k in such studies. RESULTS: We develop an optimal strategy to choose k by maximizing the statistical power of detecting differences between two sequences...
October 3, 2017: BMC Genomics
Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M Karlowski
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research...
October 3, 2017: Genome Biology
Niousha Attar, Sadegh Aliakbary
Over the past few decades, networks have been widely used to model real-world phenomena. Real-world networks exhibit nontrivial topological characteristics and therefore, many network models are proposed in the literature for generating graphs that are similar to real networks. Network models reproduce nontrivial properties such as long-tail degree distributions or high clustering coefficients. In this context, we encounter the problem of selecting the network model that best fits a given real-world network...
September 2017: Chaos
Yongkun Li, Lily He, Rong Lucy He, Stephen S-T Yau
With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny. The vectors basically consist of some typical numerical features for certain biological problems. The features may come from the primary sequences, secondary or three dimensional structures of macromolecules...
September 22, 2017: Scientific Reports
Kevin D Murray, Christfried Webers, Cheng Soon Ong, Justin Borevitz, Norman Warthmann
Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples...
September 2017: PLoS Computational Biology
Saghi Nojoomi, Patrice Koehl
BACKGROUND: Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little similarity. We have recently proposed an alignment-free method based on the concept of string kernels, SeqKernel (Nojoomi and Koehl, BMC Bioinformatics, 2017, 18:137). In this previous study, we have shown that while Seqkernel performs better than standard alignment-based methods, its applications are potentially limited, because of biases due mostly to sequence length effects...
August 25, 2017: BMC Bioinformatics
Bolin Chen, Yizhou Jiang, Xiaohui Tang, Yayue Pan, Shan Hu
The ability to print fully packaged integrated energy storage components (e.g., supercapacitors) is of critical importance for practical applications of printed electronics. Due to the limited variety of printable materials, most studies on printed supercapacitors focus on printing the electrode materials but rarely the full-packaged cell. This work presents for the first time the printing of a fully packaged single-wall carbon nanotube-based supercapacitor with direct ink writing (DIW) technology. Enabled by the developed ink formula, DIW setup, and cell architecture, the whole printing process is mask free, transfer free, and alignment free with precise and repeatable control on the spatial distribution of all constituent materials...
August 30, 2017: ACS Applied Materials & Interfaces
Evgeny V Mavrodiev, Christopher Dell, Laura Schroder
BACKGROUND: This paper is a comment on the idea of matrix-free Cladistics. Demonstration of this idea's efficiency is a major goal of the study. Within the proposed framework, the ordinary (phenetic) matrix is necessary only as "source" of Hennigian trees, not as a primary subject of the analysis. Switching from the matrix-based thinking to the matrix-free Cladistic approach clearly reveals that optimizations of the character-state changes are related not to the real processes, but to the form of the data representation...
2017: PeerJ
Bogumił M Konopka, Marta Marciniak, Witold Dyrka
BACKGROUND: The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. RESULTS: Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences...
July 17, 2017: BMC Bioinformatics
Guillaume Bernard, Cheong Xin Chan, Yao-Ban Chan, Xin-Yi Chua, Yingnan Cong, James M Hogan, Stefan R Maetschke, Mark A Ragan
We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA...
June 30, 2017: Briefings in Bioinformatics
G Persichetti, I A Grimaldi, G Testa, R Bernini
A multifunctional lab-on-a-chip platform for spectroscopic analysis of liquid samples based on an optofluidic jet waveguide is reported. The optofluidic detection scheme is achieved through the total internal reflection arising in a liquid jet of only 150 μm diameter, leading to highly efficient signal excitation and collection. This results in an optofluidic chip with an alignment-free spectroscopic detection scheme, which avoids any background from the sample container. This platform has been designed for multiwavelength fluorescence and Raman spectroscopy...
July 25, 2017: Lab on a Chip
Sharma V Thankachan, Sriram P Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru
BACKGROUND: Alignment-free sequence comparison approaches have been garnering increasing interest in various data- and compute-intensive applications such as phylogenetic inference for large-scale sequences. While k-mer based methods are predominantly used in real applications, the average common substring (ACS) approach is emerging as one of the prominent alignment-free approaches. This ACS approach has been further generalized by some recent work, either greedily or exactly, by allowing a bounded number of mismatches in the common substrings...
June 7, 2017: BMC Bioinformatics
Stephen J Bush, Mary E B McCulloch, Kim M Summers, David A Hume, Emily L Clark
BACKGROUND: The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-seq datasets could potentially be processed and integrated with newly sequenced libraries. Confounding factors in such integration include sequencing depth and methods of RNA extraction and selection. Different selection methods (typically, either polyA-selection or rRNA-depletion) omit different RNAs, resulting in different fractions of the transcriptome being sequenced...
June 13, 2017: BMC Bioinformatics
Rallis Karamichalis, Lila Kari
Summary: MoDMaps3D (Molecular Distance Maps 3D) is an alignment-free, fast, computationally lightweight webtool for computing and visualizing the interrelationships within any dataset of DNA sequences, based on pairwise comparisons between their oligomer compositions. MoDMaps3D is a general-purpose interactive webtool that is free of any requirements on sequence composition, position of the sequences in their respective genomes, presence or absence of similarity or homology, sequence length, or even sequence origin (biological or computer-generated)...
October 1, 2017: Bioinformatics
Lily He, Yongkun Li, Rong Lucy He, Stephen S-T Yau
Classification of protein are crucial topics in biology. The number of protein sequences stored in databases increases sharply in the past decade. Traditionally, comparison of protein sequences is usually carried out through multiple sequence alignment methods. However, these methods may be unsuitable for clustering of protein sequences when gene rearrangements occur such as in viral genomes. The computation is also very time-consuming for large datasets with long genomes. In this paper, based on three important biochemical properties of amino acids: the hydropathy index, polar requirement and chemical composition of the side chain, we propose a 24 dimensional feature vector describing the composition of amino acids in protein sequences...
June 3, 2017: Journal of Theoretical Biology
Fanny-Dhelia Pajuste, Lauris Kaplinski, Märt Möls, Tarmo Puurand, Maarja Lepamets, Maido Remm
We have developed a computational method that counts the frequencies of unique k-mers in FASTQ-formatted genome data and uses this information to infer the genotypes of known variants. FastGT can detect the variants in a 30x genome in less than 1 hour using ordinary low-cost server hardware. The overall concordance with the genotypes of two Illumina "Platinum" genomes is 99.96%, and the concordance with the genotypes of the Illumina HumanOmniExpress is 99.82%. Our method provides k-mer database that can be used for the simultaneous genotyping of approximately 30 million single nucleotide variants (SNVs), including >23,000 SNVs from Y chromosome...
May 31, 2017: Scientific Reports
Wenxiu Ma, Lin Yang, Remo Rohs, William Stafford Noble
Motivation: Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites...
October 1, 2017: Bioinformatics
Pooja Tripathi, Paras N Pandey
The present work employs pseudo amino acid composition (PseAAC) for encoding the protein sequences in their numeric form. Later this will be arranged in the similarity matrix, which serves as input for spectral graph clustering method. Spectral methods are used previously also for clustering of protein sequences, but they uses pair wise alignment scores of protein sequences, in similarity matrix. The alignment score depends on the length of sequences, so clustering short and long sequences together may not good idea...
May 3, 2017: Journal of Theoretical Biology
Yang Young Lu, Kujin Tang, Jie Ren, Jed A Fuhrman, Michael S Waterman, Fengzhu Sun
Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures...
May 3, 2017: Nucleic Acids Research
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