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HIGH DIMENSIONAL INDEXING FOR PROTEIN STRUCTURE MATCHING USING BOWTIES

ZI H HUANG, XIAOFANG ZHOU, DAWEI SONG
2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
We then propose a database solution by using innovative high dimensional indexing mechanisms.  ...  As 3D structures for proteins are large, complex and constantly evolving, it is very time-consuming to identify possible locations and sizes of such a matching structure for a given protein against a large  ...  The authors would like to thank Sham Prasher, Lynn Teo, Mark Smythe, Gerald Hartig and Richard Cole for their kind assistance.  ... 
doi:10.1142/9781860947322_0003 fatcat:a26fptu53zcn3l4hvd56rka6ta

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing

Marisa P. Dolled-Filhart, Michael Lee, Chih-wen Ou-yang, Rajini Rani Haraksingh, Jimmy Cheng-Ho Lin
2013 The Scientific World Journal  
For each of the three stages of (1) alignment, (2) variant calling, and (3) filtering and annotation, we describe the analysis required and survey the different software packages that are used.  ...  Furthermore, we discuss possible future developments as data sources grow and highlight opportunities for new bioinformatics tools to be developed.  ...  Some algorithms report the "best" match using heuristic approaches (e.g., BWA, Bowtie, MAQ), while others allow for all possible matches (e.g., SOAP3, SHRiMP).  ... 
doi:10.1155/2013/730210 pmid:23365548 pmcid:PMC3556895 fatcat:7n6pbn3lqbf55pmugg3pwrjdkm

FHAST: FPGA-Based Acceleration of Bowtie in Hardware

Edward B. Fernandez, Jason Villarreal, Stefano Lonardi, Walid A. Najjar
2015 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this paper, we present FHAST (FPGA hardware accelerated sequence-matching tool), a drop-in replacement for BOWTIE that uses a hardware design based on field programmable gate arrays (FPGA).  ...  FHAST is a drop-in replacement for BOWTIE, so it can be incorporated in any analysis pipeline that uses BOWTIE (e.g., TOPHAT).  ...  A preliminary version of this work was presented at the IEEE High Performance Extreme Computing Conference 2012 (HPEC'12), Waltham, CA, and appeared in its Proceedings [1] . S.  ... 
doi:10.1109/tcbb.2015.2405333 pmid:26451812 fatcat:wiur7pxna5ar5anksdfnfetsxu

Plasmonic Biosensors for Single-Molecule Biomedical Analysis

Elba Mauriz, Laura M. Lechuga
2021 Biosensors  
A special focus was devoted to new analytical developments involving a wide variety of analytes (e.g., proteins, living cells, nucleic acids and viruses).  ...  This review compiles the latest advances in plasmonic technologies for monitoring clinically relevant biomarkers at the single-molecule level.  ...  , and bowtie-nanopore compound structures ( Figure 5 ) [36] .  ... 
doi:10.3390/bios11040123 pmid:33921010 pmcid:PMC8071374 fatcat:qm6d5iwagrb4zn3p7oindknk4u

Short Read Mapping: An Algorithmic Tour

Stefan Canzar, Steven L. Salzberg
2017 Proceedings of the IEEE  
Other methods for fast indexing also emerged at this time, such as the BLAT [50] and SSAHA [93] programs, both of which (similarly to FASTA) used a hash index based on ktuples.  ...  To solve this complex, high-dimensional puzzle, reads must be mapped back to a reference genome to determine their origin Due to sequencing errors and to genuine differences between the reference genome  ...  These seeds can be matched efficiently using a structure like the FM-index and guide a coarse alignment method [19] developed for the alignment of whole genomes.  ... 
doi:10.1109/jproc.2015.2455551 pmid:28502990 pmcid:PMC5425171 fatcat:ic6d6z5ggbazdkaotcotdtbo3u

Exact Search Algorithms for Biological Sequences [chapter]

Eric Rivals, Leena Salmela, Jorma Tarhio
2010 Algorithms in Computational Molecular Biology  
Their algorithm uses two characters for indexing a two dimensional array.  ...  Second, the comparison of ZOOM or mpscan compared to genome indexing tools like Bowtie or SOAP shows that high performances are not bound to a genome index, at least for exact pattern matching.  ... 
doi:10.1002/9780470892107.ch5 fatcat:hydxzxmuhjh3zhwz7q5bdcgz74

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees

M. P. Mahmud, J. Wiedenhoeft, A. Schliep
2012 Bioinformatics  
Using a cache-oblivious kd -tree, we realize running times, which match the state-of-the-art.  ...  Using the L 1 distance between frequency vectors has the benefit of providing lower bounds for an edit distance with affine gap costs.  ...  ACKNOWLEDGEMENTS We thank Martin Frith for helping us with LAST, Martin Farach-Colton for fruitful discussion on data structures and Rajat Roy for many useful suggestions about read mappers.  ... 
doi:10.1093/bioinformatics/bts380 pmid:22962448 pmcid:PMC3436807 fatcat:gkruduuftzbijfcph7aaq63y4a

Plasmonic optical tweezers based on nanostructures: fundamentals, advances and prospects

Domna G. Kotsifaki, Síle Nic Chormaic
2019 Nanophotonics  
Making use of this unique advantage, nano-optical trapping techniques have been developed to tackle new challenges in a wide range of areas from biology to quantum optics.  ...  Another potential application of POT is its combination with graphene for studying various systems such as protein secondary structure.  ...  wavelength for the bowtie configuration [123] .  ... 
doi:10.1515/nanoph-2019-0151 fatcat:bjcn6zxp5bacdnb7axs5aerrme

Small-network approximations for geometrically frustrated Ising systems

Bilin Zhuang, Courtney Lannert
2012 Physical Review E  
Exploiting the small correlation lengths in frustrated Ising systems, we develop a method for obtaining a first approximation to the energetic properties of frustrated two-dimensional Ising systems using  ...  We also develop criteria for constructing small networks to approximate general two-dimensional frustrated Ising systems.  ...  For instance, it has been suggested that the folding of a protein into a biologically functionable structure is a result of the natural ability for the protein to resolve the frustrated couplings [21]  ... 
doi:10.1103/physreve.85.031107 pmid:22587038 fatcat:dpurg2dmznb7ll3vt2ed5tsuoy

Optical integrated chips with micro and nanostructures for refractive index and SERS-based optical label-free sensing

Liu Liu, Mingliang Jin, Yaocheng Shi, Jiao Lin, Yuan Zhang, Li Jiang, Guofu Zhou, Sailing He
2015 Nanophotonics  
In order to improve the extraction efficiency of the Raman signal at a high wave number, a nano-bowtie array substrate is fabricated, which exhibits double resonances at both the excitation wavelength  ...  platforms for label-free optical biosensors.  ...  A detection limit of 20 pM for proteins was demonstrated.  ... 
doi:10.1515/nanoph-2015-0015 fatcat:eo2u5bthhrhknlrt3csm3s4wua

3D Protein Structure Matching by Patch Signatures [chapter]

Zi Huang, Xiaofang Zhou, Heng Tao Shen, Dawei Song
2006 Lecture Notes in Computer Science  
For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have one or more matching structural regions called patches.  ...  As 3D structures for proteins are large, complex and constantly evolving, it is computationally expensive and very time-consuming to identify possible locations and sizes of patches for a given protein  ...  DP0663272) and the Co-operative Centre for Enterprise Distributed Systems Technology (DSTC) through the Australian Federal Government's CRC Programme (Department of Education, Science and Training).  ... 
doi:10.1007/11827405_52 fatcat:tijxzw4x7vfcfjegnp5u2sqnou

Computational biology in the 21st century

Bonnie Berger, Noah M. Daniels, Y. William Yu
2016 Communications of the ACM  
substring index, based on the BWT, which provides efficient storage as well as fast search. 3 BWA (Burrows-Wheeler Aligner) uses the BWT, while the Bowtie 2 mapper further relies on the FM-index for  ...  probabilistic approaches, the high dimensionality and noise in the data present significant challenges.  ...  Page 18 Metric-entropy ratio (ratio of clusters to entries in database) and fractal dimension at typical search radii for four datasets  ... 
doi:10.1145/2957324 pmid:28966343 pmcid:PMC5615407 fatcat:h33qu34kdvehjldnbvvvgnrnqq

Interdisciplinary nanophotonics

Enzo Di Fabrizio, Mark Stockman
2019 Nanophotonics  
It also demonstrated that the modulator utilizing strong index-change from both real and imaginary parts of active material enables compact and high-performing modulators using semiconductor foundry-near  ...  This is used to achieve optimal matching between the electromagnetic field profile and the depletion regions of the p-n junction.  ... 
doi:10.1515/nanoph-2019-0236 fatcat:tjskscztlrhhxozmtfvqs4aklq

Optical Fiber, Nanomaterial, and THz-Metasurface-Mediated Nano-Biosensors: A Review

B M Azizur Rahman, Charusluk Viphavakit, Ratchapak Chitaree, Souvik Ghosh, Akhilesh Kumar Pathak, Sneha Verma, Natsima Sakda
2022 Biosensors  
The increasing use of nanomaterials and scalable, high-yield nanofabrication process are revolutionizing the development of novel biosensors.  ...  nanostructures, such as nanosphere, nanorods, nanofiber, core–shell nanoparticles, nanotubes, and thin films, have been exploited to enhance the detectability of labelled or label-free biological molecules with a high  ...  = 1.3 to 1.8 to match the refractive index of the protein.  ... 
doi:10.3390/bios12010042 pmid:35049670 pmcid:PMC8773603 fatcat:q37y4r2lpjfnthcauloyh2x3ou

Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures

Kelly Patrick Stanton, Fabio Parisi, Francesco Strino, Neta Rabin, Patrik Asp, Yuval Kluger
2013 Nucleic Acids Research  
This allows us to efficiently compare numerous chromatin-immunoprecipitation sequencing (ChIP-seq) data sets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions  ...  Data compression techniques are needed for efficient comparisons of a new genomic experiment with large repositories of publicly available profiles.  ...  ACKNOWLEDGEMENTS The authors thank Ronen Talmon, Sherman Weissman, Ronald Coifman and Paolo Barbano for insightful discussions.  ... 
doi:10.1093/nar/gkt627 pmid:23873955 pmcid:PMC3763565 fatcat:2pjwybroorhcdnhg2mxkjmuusq
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