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Genoogle: an indexed and parallelized search engine for similar DNA sequences [article]

Felipe Albrecht
2015 arXiv   pre-print
The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required time anymore.  ...  This work aims to use data indexing techniques to reduce the searching process computation cost united with the parallelization of the searching techniques to use the computational capacity of the multi  ...  parallelization, it still have a linear computation complexity.  ... 
arXiv:1507.02987v1 fatcat:sx7vv2jravbxhhwcpfooc3xtwi

From Persistent Homology to Reinforcement Learning with Applications for Retail Banking [article]

Jeremy Charlier
2019 arXiv   pre-print
First, we highlight how to overcome insufficient financial data by generating artificial data using generative models and persistent homology.  ...  In this context, we investigate in this thesis different concepts bridging the gap between persistent homology, neural networks, recommender engines and reinforcement learning with the aim of improving  ...  We compare VecHGrad with ten different algorithms applied to the three main tensor decomposition with increasing linear algebra complexity, CP/PARAFAC, DEDICOM and PARATUCK2: • ALS, Alternating Least Squares  ... 
arXiv:1911.11573v1 fatcat:ubyllsyzxne6dd63xah5ggvoam


2014 International Journal of Computer Science and Informatics  
Its importance is intensed by large amounts of sequence data coming from PDB (Protein Data Bank) and the fact that experimentally methods such as X-ray crystallography or Nuclear Magnetic Resonance (NMR  ...  Thus, protein structure is a fundamental area of computational biology.  ...  Protein threading prediction can used for protein structure prediction when 1) The target protein does not share a high sequence similarity with any protein in PDB (protein data bank) 2) The target protein  ... 
doi:10.47893/ijcsi.2014.1168 fatcat:ioiplznc6zarjlfcbw6hggcmxi

Local Homology of Word Embeddings [article]

Tadas Temčinas
2018 arXiv   pre-print
We describe a parallelisable unsupervised learning algorithm based on local homology of datapoints and show some experimental results on word embedding data.  ...  We see that local homology of datapoints in word embedding data contains some information that can potentially be used to solve the word sense disambiguation problem.  ...  Let us discuss an algorithm that computes k-th local homology with coefficients in Z/2Z.  ... 
arXiv:1810.10136v1 fatcat:vzxkyvuwpjckxgcrncgqygryo4

The interactome: Predicting the protein-protein interactions in cells

Dariusz Plewczyński, Krzysztof Ginalski
2009 Cellular & Molecular Biology Letters  
The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.  ...  Protein complexes are better preserved during the evolution process than single proteins, so some computational methods focus on the prediction or searching of complexes that are common to several species  ...  The InterPreTS server, given a pair of query sequences, searches for homologs in a database of interacting domains (DBID) of known three-dimensional complex  ... 
doi:10.2478/s11658-008-0024-7 pmid:18839074 fatcat:zzfjqkrutrgszpopzh3z6f2xce

Survey on index based homology search algorithms

Xianyang Jiang, Peiheng Zhang, Xinchun Liu, Stephen S.-T. Yau
2007 Journal of Supercomputing  
As a whole, the paper provides a survey on index based homology search algorithms.  ...  This is especially true for index based homology search algorithms. The paper briefly introduces main index construction methods.  ...  However, homology search or similarity computation has a time complexity of either linear or quadratic to the length of the sequences (or database) involved.  ... 
doi:10.1007/s11227-006-0041-0 fatcat:hhijz2rah5a5jcbu4d6ecj3npi

Characterizing Protein Conformational Spaces using Efficient Data Reduction and Algebraic Topology

Arpita Joshi, Nurit Haspel, Eduardo González
2022 Journal of Human Earth and Future  
Representing the structures with fewer attributes that capture the most variance in the data makes for a quicker and more precise analysis of these structures.  ...  Datasets representing the conformational landscapes of protein structures are high-dimensional and hence present computational challenges.  ...  The search begins with the PDB (Protein Data Bank) format of one conformational extreme and expands following a biased Rapidly-expanding Random Tree (RRT) algorithm to simulate the pathway that can be  ... 
doi:10.28991/hef-sp2022-01-01 fatcat:yzv2jdhvxbg35cllhcbtiktiq4

Characterizing Protein Conformational Spaces using Dimensionality Reduction and Algebraic Topology [article]

Arpita Joshi, Nurit Haspel, Eduardo Gonzalez
2021 bioRxiv   pre-print
Representing the structures with fewer attributes that capture the most variance of the data, makes for quicker and precise analysis of these structures.  ...  Datasets representing the conformational landscapes of protein structures are high dimensional and hence present computational challenges.  ...  The search begins with the PDB (Protein Data Bank) format of one conformational extreme and expands following a biased Rapidly-expanding Random Tree (RRT) algorithm to simulate the pathway that can be  ... 
doi:10.1101/2021.11.16.468545 fatcat:aofpyw75qrh7li5p4svh6ngsty


1998 Trends in Biotechnology  
DUST -Program for filtering low-complexity regions of DNA structure.  ...  The number of distinct alignments, with score equivalent to or better than the one of interest, that are expected to occur in a database search purely by chance.  ...  An iterative search that uses the BLAST algorithm to provide fast searches, and builds a profile at every iteration.  ... 
doi:10.1016/s0167-7799(98)00136-x fatcat:mwgzfif7qfbu3bp3decsod2rhq

Assessment of Accuracies of Protein 3-Dimensional Prediction Software

Rijad Gosto
2018 Southeast Europe Journal of Soft Computing  
The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search (Nielsen, et. Al., 2010) .  ...  RaptorX is a protein structure prediction server developed by Xu group, excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB).  ... 
doi:10.21533/scjournal.v7i2.161 fatcat:54jhfbam5jhllbljlgxu3zdlna

Computational biology in the 21st century

Bonnie Berger, Noah M. Daniels, Y. William Yu
2016 Communications of the ACM  
Computer scientists routinely exploit the structure of various data in order to reduce time or space complexity. In computational biology, this approach has implicitly served researchers well.  ...  The homology search problem was believed to be solved previously; Basic Local Alignment Search Tool (BLAST) 3 has been the standard tool for performing homology (similarity) search on databases of nucleotide  ...  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

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

Krishna Praneeth Kilambi, Michael S. Pacella, Jianqing Xu, Jason W. Labonte, Justin R. Porter, Pravin Muthu, Kevin Drew, Daisuke Kuroda, Ora Schueler-Furman, Richard Bonneau, Jeffrey J. Gray
2013 Proteins: Structure, Function, and Bioinformatics  
For α-repeat Rep4-Rep2 and g-type lysozyme-PliG inhibitor complexes, homology models were built and standard and pH-sensitive docking algorithms were used to generate structures with interface RMSD values  ...  The diversity of problems at hand requires computational algorithms to be versatile; the recent additions to the Rosetta suite expand the capabilities to encompass more biologically realistic docking problems  ...  We thank the crystallographers who offered their complexes as the CAPRI targets.  ... 
doi:10.1002/prot.24425 pmid:24123494 pmcid:PMC4037910 fatcat:s6twuc7tgzeyzgv3ncwua7hlxm

Proteo3Dnet: a web server for the integration of structural information with interactomics data

Guillaume Postic, Jessica Andreani, Julien Marcoux, Victor Reys, Raphaël Guerois, Julien Rey, Emmanuelle Mouton-Barbosa, Yves Vandenbrouck, Sarah Cianferani, Odile Burlet-Schiltz, Gilles Labesse, Pierre Tufféry
2021 Nucleic Acids Research  
This is achieved using three means: (i) the search for interologs with resolved structure available in the protein data bank, including cross-species remote homology search, (ii) the search for possibly  ...  weaker interactions mediated through Short Linear Motifs as predicted by ELM-a unique feature of Proteo3Dnet, (iii) the search for protein-protein interactions physically validated in the BioGRID database  ...  ACKNOWLEDGEMENTS The authors would like to thank Célia Plisson-Chastang, for careful proof-reading of the pre-40S data analysis.  ... 
doi:10.1093/nar/gkab332 pmid:33963857 pmcid:PMC8262742 fatcat:lfvlhqzsy5drtl6gvua4jmrvaq

Integrating Cross-Linking Experiments with Ab Initio Protein–Protein Docking

Thom Vreven, Devin K. Schweppe, Juan D. Chavez, Chad R. Weisbrod, Sayaka Shibata, Chunxiang Zheng, James E. Bruce, Zhiping Weng
2018 Journal of Molecular Biology  
We tested our approach using 19 cases that resulted from an exhaustive search of the Protein Data Bank for protein complexes with crosslinks identified in our experiments.  ...  The dataset was searched against the known structures in the Protein Data Bank [35] and yielded 19 test cases.  ...  Integrating computational algorithms with lowerresolution experimental data can improve the accuracy of protein complex structures algorithms are designed to predict such complexes.  ... 
doi:10.1016/j.jmb.2018.04.010 pmid:29665372 pmcid:PMC6084434 fatcat:5ie7meonr5ekvelw4qnlplbgba

Finding and Characterizing Repeats in Plant Genomes [chapter]

Jacques Nicolas, Pierre Peterlongo, Sébastien Tempel
2016 Msphere  
Indeed, it may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of the search for repeats and more complex patterns.  ...  the large--scale search of these structures.  ...  It is possible to decrease this complexity for a linear behavior, although it will always depend of the size of the bank.  ... 
doi:10.1007/978-1-4939-3167-5_17 pmid:26519414 fatcat:j47bdlqwibhxzifuzkfccppuve
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