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Yuxin Qiao, Xiaoyan Zhao, Jun Zhu, Ran Tu, Libing Dong, Li Wang, Zhiyang Dong, Qinhong Wang, Wenbin Du
Lipases are ubiquitous enzymes of great physiological significance that have been used extensively in multiple industries. Environmental microorganisms are a major source for the discovery of novel lipases with high catalytic efficiency and selectivity. However, current plate-based screening of lipase-producing strains is time consuming, labour intensive and inefficient. In this study, we developed an ultra-high throughput screening pipeline for lipase-producing strains based on fluorescence-activated droplet sorting (FADS) using a compact optical system that could be easily set up in an alignment-free manner...
December 11, 2017: Lab on a Chip
Brian B Luczak, Benjamin T James, Hani Z Girgis
Motivation: Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. Results: We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares...
December 6, 2017: Briefings in Bioinformatics
Yuki Kato, Jan Gorodkin, Jakob Hull Havgaard
BACKGROUND: Structured non-coding RNAs play many different roles in the cells, but the annotation of these RNAs is lacking even within the human genome. The currently available computational tools are either too computationally heavy for use in full genomic screens or rely on pre-aligned sequences. METHODS: Here we present a fast and efficient method, DotcodeR, for detecting structurally similar RNAs in genomic sequences by comparing their corresponding coarse-grained secondary structure dot plots at string level...
December 2, 2017: BMC Genomics
Jan Dreher, Josef Scheiber, Nikolaus Stiefl, Knut Baumann
A novel alignment-free molecular descriptor called xMaP (flexible MaP descriptor) is introduced. The descriptor is the advancement of the previously published translationally and rotationally invariant 3D descriptor MaP (Mapping Property distributions onto the molecular surface) to the 4th dimension. In addition to MaP, xMaP is independent of the chosen starting conformation of the encoded molecules and is therefore entirely alignment-free. This is achieved by using ensembles of conformers, which are generated by conformational searches...
November 27, 2017: Journal of Chemical Information and Modeling
Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele Calogero, Simone Ferrero, Francesca Cordero
BACKGROUND: Mantle Cell Lymphoma (MCL) is a B cell aggressive neoplasia accounting for about the 6% of all lymphomas. The most common molecular marker of clonality in MCL, as in other B lymphoproliferative disorders, is the ImmunoGlobulin Heavy chain (IGH) rearrangement, occurring in B-lymphocytes. The patient-specific IGH rearrangement is extensively used to monitor the Minimal Residual Disease (MRD) after treatment through the standardized Allele-Specific Oligonucleotides Quantitative Polymerase Chain Reaction based technique...
November 23, 2017: BMC Bioinformatics
Jagadesan Sankarasubramanian, Udayakumar S Vishnu, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
Brucellosis is an important zoonotic disease caused by Brucella spp. We present a phylogeny of 552 strains based on genome-wide single nucleotide polymorphisms (SNPs) determined by an alignment-free k-mer approach. A total of 138,029 SNPs were identified from 552 Brucella genomes. Of these, 31,152 and 106,877 were core and non-core SNPs, respectively. Based on pan-genome analysis 11,937 and 972 genes were identified as pan and core genome, respectively. The pan-genome-wide analysis studies (Pan-GWAS) could not identify the group-specific variants in Brucella spp...
November 15, 2017: Infection, Genetics and Evolution
Yifei Zhang, Alexander V Alekseyenko
The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data...
2017: PloS One
Jianyu Zhou, Shining Ma, Dongfang Wang, Jianyang Zeng, Tao Jiang
Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for estimating exon-inclusion ratios at the genome scale all require the existence of a reference transcriptome. In this paper, we propose an alignment-free method, FreePSI, to perform genome-wide estimation of exon-inclusion ratios from RNA-Seq data without relying on the guidance of a reference transcriptome...
November 9, 2017: Nucleic Acids Research
Fazle E Faisal, Khalique Newaz, Julie L Chaney, Jun Li, Scott J Emrich, Patricia L Clark, Tijana Milenković
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D contact approaches study 3D structures directly and are alignment-based. Instead, 3D structures can be modeled as protein structure networks (PSNs). Then, network approaches can compare proteins by comparing their PSNs. These can be alignment-based or alignment-free. We focus on the latter...
November 2, 2017: Scientific Reports
Hyein Seo, Dong-Ho Cho
The sequence comparison is an important part in bioinformatics to understand the biological property of genome. Although the alignment based sequence comparison is traditional and reliable algorithm, alignment free methods have been actively researched because of their advantage in terms of computational complexity. In this paper, we suggest a new alignment free genome comparison scheme based on statistical approach. From sequence components, word frequency information of the sequence is estimated. By investigating the relationship between estimated frequency information and actual word frequency, the characteristics of the sequence are numerically represented...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Yong-Joon Song, Dong-Ho Cho
In order to extract phylogenetic information from DNA sequences, alignment-free methods and alignment-based methods are used. Alignment-based methods have high complexity and conventional alignment-free methods have low accuracy. In this paper, a new alignment-free method based on the distribution of repeated k-word measure is proposed. This novel measure is based on k-words and its multiple repeated words. We can get higher performance than conventional word count methods in case of using proposed scheme while maintaining total time complexity...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Gyu-Bum Han, Byung Chang Chung, Dong-Ho Cho
This paper proposes a novel alignment-free sequence comparison method to identify the genetic relationships of organisms with a high resolution. For an accurate comparison, both frequency and position information of k-words are obtained from genome sequences in the proposed alignment-free sequence comparison method. Using principal component analysis (PCA) and phylogeny analysis, we identify the classification performance of proposed method. Then, the phylogenetic trees of proposed and conventional schemes are compared with reliable reference tree...
July 2017: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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
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