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22nd Iranian Conference on Electrical Engineering (ICEE)

作者： Mahmoodi, Mohammad Reza Nikaein, Hossein Fahimi, Zahra Isfahan Univ Technol Dept Elect & Comp Engn Esfahan Iran

ISBN: (纸本)9781479944095

Undoubtedly, Basic Local Alignment Search Tool is one of the most prevalent algorithms in sequence searching and bioinformatics. blast is an index-based approach in order to recognize an unknown string of DNA sequence and due to its high computational nature, different types of hardware configurations have been proposed. In this paper, the traditional algorithm is applied;however a new architecture is proposed to speed up the algorithm. The design consists of a workstation and a FPGA as an accelerator. The system is based on 41 parallel cores implemented on Xilinx XC4VFX100 FPGA device. The most appealing features of this design are its speed and long input streams. Queries and subjects up to thousands of characters are processed in this architecture and it is verified to be 75.1 faster than NCBI software run at 3GHz, Pentium4 system.

关键词： FPGA Sequence Searching blast algorithm Hardware Implementation

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A novel video retrieval algorithm based on coarse-grained and fine-grained

A novel video retrieval algorithm based on coarse-grained an...

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11th International Conference on Wireless Communications, Networking and Mobile Computing (WiCOM 2015)

作者： Xu Jie Aiyun Xie Yumeng Peng Sun Jian Key Lab of Optical Fiber Sensing and Communications (Ministry of Education) School of Communication and Information Engineering University of Electronic Science and Technology of China Chengdu 611731 China

ISBN: (纸本)9781510821279

In order to solve the balance problems between efficiency and accuracy encountered in content-based video retrieval, in this paper, we propose firstly a video retrieval scheme based on coarse granularity. To achieve the coarse-grained video retrieval, we use inverted index. Further, we expose an improved blast algorithm to realize fine-grained retrieval of video fingerprint. Finally, simulation results show the good efficiency and accuracy of the algorithm we have proposed. Therefore, this algorithm provides effective technical support for the security regulation and quick retrieval of Internet video.

关键词： blast algorithm Coarse-Grained Fine-Grained Inverted Index Video retrieval video retrieval microparticles Inverted files coarse-grained materials Balance impairment

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2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers

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PLOS COMPUTATIONAL BIOLOGY 2014年第5期10卷 e1003621页

作者： Fogg, Christiana N. Kovats, Diane E. Int Soc Computat Biol La Jolla CA USA

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blast: B-LAyered bad-character SHIFT tables for high-speed pattern matching

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IET INFORMATION SECURITY 2013年第3期7卷 195-202页

作者： Choi, Yoon-Ho Seo, Seung-Woo Kyonggi Univ Dept Convergence Secur Suwon 443370 South Korea Seoul Natl Univ Sch Elect Engn & Comp Sci Seoul 151744 South Korea

In this study, the authors propose a new multi-pattern matching algorithm, called blast (B-LAyered bad-character Shift Tables with a single-byte search unit), which considers space-time tradeoff in the context of shift values during the search. Here, the term bad character' is a character that causes a mismatch. While checking multiple bytes in scanning the text at a time, the blast algorithm overcomes the reduction of the average shift value in a typical search, which is caused by the dependency on the multi-byte search unit (MBSU) and the large frequency of the last character of the given patterns. From the theoretical analysis, the authors validate the correctness of the blast algorithm. Also, from the experimental results across different setups, the authors show that the blast algorithm provides the faster search time than the other algorithms. For example, the authors obtain an enhancement by as much as 212.41% on average for various numbers of attack patterns and attack traffic conditions compared with that of the modified Wu-Manber algorithm. In addition, it is shown that the blast algorithm drastically reduces the amount of memory required for constructing the shift table based on a MBSU from 64 KB to 1 KB.

关键词： search problems string matching text analysis computer network security B-layered bad-character SHIFT tables high-speed pattern matching multipattern matching algorithm space-time tradeoff shift values blast algorithm text scanning byte checking single-byte search unit single bad-character SHIFT table multibyte search unit MBSU pattern search time attack patterns attack traffic conditions Wu-Manber algorithm

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Structural Consensus among Antibodies Defines the Antigen Binding Site

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PLOS COMPUTATIONAL BIOLOGY 2012年第2期8卷 e1002388-e1002388页

作者： Kunik, Vered Peters, Bjoern Ofran, Yanay Bar Ilan Univ Goodman Fac Life Sci Ramat Gan Israel La Jolla Inst Allergy & Immunol Div Vaccine Discovery La Jolla CA USA

The Complementarity Determining Regions (CDRs) of antibodies are assumed to account for the antigen recognition and binding and thus to contain also the antigen binding site. CDRs are typically discerned by searching for regions that are most different, in sequence or in structure, between different antibodies. Here, we show that,20% of the antibody residues that actually bind the antigen fall outside the CDRs. However, virtually all antigen binding residues lie in regions of structural consensus across antibodies. Furthermore, we show that these regions of structural consensus which cover the antigen binding site are identifiable from the sequence of the antibody. Analyzing the predicted contribution of antigen binding residues to the stability of the antibody-antigen complex, we show that residues that fall outside of the traditionally defined CDRs are at least as important to antigen binding as residues within the CDRs, and in some cases, they are even more important energetically. Furthermore, antigen binding residues that fall outside of the structural consensus regions but within traditionally defined CDRs show a marginal energetic contribution to antigen binding. These findings allow for systematic and comprehensive identification of antigen binding sites, which can improve the understanding of antigenic interactions and may be useful in antibody engineering and B-cell epitope identification.

关键词： Sequence alignment blast algorithm Binding analysis Alanine Antigens T cell receptors Built structures Protein structure

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Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

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PLOS COMPUTATIONAL BIOLOGY 2012年第6期8卷 e1002358-e1002358页

作者： Abubucker, Sahar Segata, Nicola Goll, Johannes Schubert, Alyxandria M. Izard, Jacques Cantarel, Brandi L. Rodriguez-Mueller, Beltran Zucker, Jeremy Thiagarajan, Mathangi Henrissat, Bernard White, Owen Kelley, Scott T. Methe, Barbara Schloss, Patrick D. Gevers, Dirk Mitreva, Makedonka Huttenhower, Curtis Washington Univ Sch Med Genome Inst St Louis MO 63130 USA Harvard Univ Sch Publ Hlth Dept Biostat Boston MA 02115 USA J Craig Venter Inst Rockville MD USA Univ Michigan Dept Microbiol & Immunol Ann Arbor MI 48109 USA Forsyth Inst Dept Mol Genet Cambridge MA USA Harvard Univ Sch Dent Med Dept Oral Med Infect & Immun Boston MA 02115 USA Univ Maryland Sch Med Inst Genome Sci Baltimore MD 21201 USA Broad Inst MIT & Harvard Cambridge MA USA Univ Mediterranee UMR CNRS 6098 Marseille France San Diego State Univ Dept Biol San Diego CA 92182 USA

Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://***/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads,

关键词： Metagenomics Microbiome Metabolic pathways blast algorithm Community structure Community ecology Biological transport Enzyme metabolism

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Gene Network Homology in Prokaryotes Using a Similarity Search Approach: Queries of Quorum Sensing Signal Transduction

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PLOS COMPUTATIONAL BIOLOGY 2012年第8期8卷 e1002637-e1002637页

作者： Quan, David N. Bentley, William E. Univ Maryland Fischell Dept Bioengn College Pk MD 20742 USA Inst Biosci & Biotechnol Res College Pk MD USA

Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers. Importantly, autoinducer-2 (AI-2) is synthesized via the enzyme LuxS in over 80 species, some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner. AI-2 mediated phenotypes are not well understood however, as the means for signal transduction appears varied among species, while AI-2 synthesis processes appear conserved. Approaches to reveal the recognition pathways of AI-2 will shed light on pathogenicity as we believe recognition of the signal is likely as important, if not more, than the signal synthesis. LMNAST (Local Modular Network Alignment Similarity Tool) uses a local similarity search heuristic to study gene order, generating homology hits for the genomic arrangement of a query gene sequence. We develop and apply this tool for the E. coli lac and LuxS regulated (Lsr) systems. Lsr is of great interest as it mediates AI-2 uptake and processing. Both test searches generated results that were subsequently analyzed through a number of different lenses, each with its own level of granularity, from a binary phylogenetic representation down to trackback plots that preserve genomic organizational information. Through a survey of these results, we demonstrate the identification of orthologs, paralogs, hitchhiking genes, gene loss, gene rearrangement within an operon context, and also horizontal gene transfer (HGT). We found a variety of operon structures that are consistent with our hypothesis that the signal can be perceived and transduced by homologous protein complexes, while their regulation may be key to defining subsequent phenotypic behavior.

关键词： lac operon Phylogenetics blast algorithm Horizontal gene transfer Operons Database searching Quorum sensing Regulons

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PMD compensation in multilevel coded-modulation schemes with coherent detection using blast algorithm and iterative polarization cancellation

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OPTICS EXPRESS 2008年第19期16卷 14845-14852页

作者： Djordjevic, Ivan B. Xu, Lei Wang, Ting Univ Arizona Dept Elect & Comp Engn Tucson AZ 85721 USA NEC Labs Amer Princeton NJ 08540 USA

We present two PMD compensation schemes suitable for use in multilevel (M >= 2) block-coded modulation schemes with coherent detection. The first scheme is based on (a) under bar blast-type polarization-interference cancellation scheme, and the second scheme is based on iterative polarization cancellation. Both schemes use the LDPC codes as channel codes. The proposed PMD compensations schemes are evaluated by employing coded-OFDM and coherent detection. When used in combination with girth-10 LDPC codes those schemes outperform polarization-time coding based OFDM by 1 dB at BER of 10(-9), and provide two times higher spectral efficiency. The proposed schemes perform comparable and are able to compensate even 1200 ps of differential group delay with negligible penalty. (C) 2008 Optical Society of America.

关键词： .Multilevel LDPC Coherent Detection girth proposed schemes spectral efficiency polarization interference blast algorithm polarization cancellation PMD compensation schemes cancellation scheme

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Ten Simple Rules for Teaching Bioinformatics at the High School Level

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PLOS COMPUTATIONAL BIOLOGY 2011年第10期7卷 1-2页

作者： Form, David Lewitter, Fran Nashoba Reg High Sch Dept Sci Bolton MA USA Whitehead Inst Cambridge MA 02142 USA

The authors reflect on bioinformatics education at the secondary level. They provide various guidelines for science teachers which include excluding any irrelevant information, linking concepts with real-life examples and encouraging students to do subject-based activities on their own. Supplementary teaching curriculum examples for teachers are also provided.

关键词： Bioinformatics Schools blast algorithm Human learning Evolutionary genetics Obesity Protein structure comparison RNA structure

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A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

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PLOS COMPUTATIONAL BIOLOGY 2011年第10期7卷 1-7页

作者： Gallagher, Suzanne Renick Coon, William Donley, Kristin Scott, Abby Goldberg, Debra S. Univ Colorado Dept Comp Sci Boulder CO 80309 USA Boulder Valley Sch Dist Boulder CO USA

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum. We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://***/?page_id=149#biology or by contacting the authors. Author Summary We have designed and implemented a curriculum to teach basic computational biology to advanced high school stud

关键词： blast algorithm Computational biology Schools Teachers Computer and information sciences Phylogenetic analysis Biologists Human learning

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