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Engineering Motif Search for Large Motifs

Petteri Kaski, Juho Lauri, Suhas Thejaswi, Marc Herbstritt
2018 Symposium on Experimental and Efficient Algorithms  
This scalability to large graphs prompts the dual question whether it is possible to scale to large motif sizes.  ...  of at most k/2 b−1 for a connected m-edge input and a motif of size k.  ...  Motif Search for Large Motifs Al-Naffouri, Han, and Chung [25] .  ... 
doi:10.4230/lipics.sea.2018.28 dblp:conf/wea/KaskiLT18 fatcat:nb5mcmsod5hzji4elhqrawfkqm

Engineering Motif Search for Large Graphs [chapter]

Andreas Björklund, Petteri Kaski, Lukasz Kowalik, Juho Lauri
2014 2015 Proceedings of the Seventeenth Workshop on Algorithm Engineering and Experiments (ALENEX)  
all 2 V(H) Iteration, for all = 2, 3, . . . , k and all 2 V(H) Motif search Data, query, and one match Limited background on motif search • Extension of jumbled pattern matching on strings (=paths)  ...  Starting point (theory): Õ(2 k k 2 m)-time randomized algorithm for graph motif (decides existence of match)  ...  v) LINE_MUL(p, pul1, pvl2); LINE_ADD(s, s, p); } Iteration, for all = 2, 3, . . . , k and all 2 V(H) Compiled inner loop (w/ AVX2 +PCLMULQDQ)  ... 
doi:10.1137/1.9781611973754.10 dblp:conf/alenex/BjorklundKKL15 fatcat:qrgubbsdorbqzloznee6hbztiy

Discovering common motifs in cursor movement data for improving web search

Dmitry Lagun, Mikhail Ageev, Qi Guo, Eugene Agichtein
2014 Proceedings of the 7th ACM international conference on Web search and data mining - WSDM '14  
In order to scale our approach to realistic datasets, we introduce novel optimizations for motif discovery, specifically designed for mining cursor movement data.  ...  tasks, compared to a state-ofthe-art baseline that relies on extensive feature engineering.  ...  USING MOTIFS FOR RELEVANCE PRE-DICTION AND RANKING Estimation of document relevance from large scale user behavior data is of critical importance to Web search engines.  ... 
doi:10.1145/2556195.2556265 dblp:conf/wsdm/LagunAGA14 fatcat:3mhdutdeyna27iaywukze7li7q

A Real-Time All-Atom Structural Search Engine for Proteins

Gabriel Gonzalez, Brett Hannigan, William F. DeGrado, Andreas Prlic
2014 PLoS Computational Biology  
Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine.  ...  To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system.  ...  The search engine may also optionally specify a search timeout to further reduce server load for users that request a large number of search results.  ... 
doi:10.1371/journal.pcbi.1003750 pmid:25079944 pmcid:PMC4117414 fatcat:6alijvev2zd27iufhdswivw5xm

Different Users, Different Opinions

Yiqun Liu, Ye Chen, Jinhui Tang, Jiashen Sun, Min Zhang, Shaoping Ma, Xuan Zhu
2015 Proceedings of the 38th International ACM SIGIR Conference on Research and Development in Information Retrieval - SIGIR '15  
motifs extracted from mouse movement data on search result pages (SERPs).  ...  Besides the existing frequency-based motif selection method, two novel selection strategies (distance-based and distribution-based) are also adopted to extract high quality motifs for satisfaction prediction  ...  Similarly, for motifs in M DSAT , we have: (1) and (2) , we can select motifs with large difference from the motifs in the other kind of sessions, which have large chances to be predictive ones.  ... 
doi:10.1145/2766462.2767721 dblp:conf/sigir/LiuCTS0MZ15 fatcat:ebiihfio2nbpxhgctvn3ef6gu4

MoMo: Discovery of post-translational modification motifs [article]

Alice Cheng, Charles Grant, Timothy L. Bailey, William Noble
2017 bioRxiv   pre-print
In addition to reading sequence files in FASTA format, MoMo is capable of directly parsing output files produced by commonly used mass spectrometry search engines.  ...  Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. MoMo is a software tool for identifying motifs among sets of PTMs.  ...  Importantly, to enhance usability, the portal works directly with database search results files produced by popular mass spectrometry search engines, including Comet, MS-GF+, Tide, etc.  ... 
doi:10.1101/153882 fatcat:kwilznglvzfazc47dqnmbxhd5i

A new algorithm for performing three-dimensional searches of the Cambridge Structural Database

James A. Chisholm, Sam Motherwell
2004 Journal of Applied Crystallography  
Performance metrics are presented for example searches composed of several substructures and several intermolecular connections.  ...  It is shown that such searches, which are outside the capabilities of current search engines, can now be performed on the entire Cambridge Structural Database with search times of around half an hour.  ...  For example, the task of identifying extended hydrogenbond ring motifs can take several hours or even days with ConQuest, and the search engine will not identify all occurrences of the motif.  ... 
doi:10.1107/s0021889804002924 fatcat:mofvmufly5fvjogmjpvwe4fgmy

DeepFinder: An integration of feature-based and deep learning approach for DNA motif discovery

Nung Kion Lee, Farah Liyana Azizan, Yu Shiong Wong, Norshafarina Omar
2018 Biotechnology & Biotechnological Equipment  
This indicates the effectiveness and potential of our proposed DeepFinder for large-scale motif analysis.  ...  The threestage approach uses only a subset of input sequences for initial motif prediction, and the initial motifs obtained are employed for site detection in the remaining input subset of non-overlaps  ...  Early methods for genome-wide motif discovery are based on comparative genomic [2] and motif profile search.  ... 
doi:10.1080/13102818.2018.1438209 fatcat:djfsm4zpzjaajhmqyz2q4dizay

Web Appearance Disambiguation of Personal Names Based on Network Motif

Kai-hsiang Yang, Kun-yan Chiou, Hahn-ming Lee, Jan-ming Ho
2006 2006 IEEE/WIC/ACM International Conference on Web Intelligence (WI 2006 Main Conference Proceedings)(WI'06)  
Searching for information about a particular person is a common activity on search engines. However, current search engines do not provide any special function for search a person.  ...  The key idea of the WAD system is to find out smaller node motifs as evidences of close relationship between pages for clustering searched web pages.  ...  Introduction Searching for personal information is one of the most popular search types for search engines.  ... 
doi:10.1109/wi.2006.189 dblp:conf/webi/YangCLH06 fatcat:y32o3f3hpbclpnrpcvxdsadn7y

Learning Functions in Large Networks requires Modularity and produces Multi-Agent Dynamics [article]

C. H. Huck Yang, Rise Ooi, Tom Hiscock, Victor Eguiluz, Jesper Tegnér
2018 arXiv   pre-print
While our algorithm successfully learns large functional motifs, we identify a threshold size of approximately 20 nodes beyond which learning breaks down.  ...  To end this, we introduce a gradient descent machine learning (ML) approach and genetic algorithms to learn larger functional motifs in contrast to an (unfeasible) exhaustive search.  ...  The crossover action ensures the cost function to be convex in a large search space where the search of the desired weights correspond to the network motifs.  ... 
arXiv:1807.03001v2 fatcat:lhzrd7bo2zdzlnmdkikcl5m5ra

An Intuitive Wizard to Identify Pattern in Similarity Expressed Gene Set of Rice

Preeti Barrow, Swathi Naryanan
2018 International Journal of Intelligent Engineering and Systems  
Further, to search for already known motifs parallel version of adaptive hash based pattern matching algorithm has been implemented.  ...  expression patterns (motifs) for the queried genes.  ...  suitable for short patterns and large alphabets.  ... 
doi:10.22266/ijies2018.0831.01 fatcat:fc5mt5vkr5ffhnmfvo37smigyy

Systematic Reverse Engineering of Network Topologies: A Case Study of Resettable Bistable Cellular Responses

Debasish Mondal, Edward Dougherty, Abhishek Mukhopadhyay, Adria Carbo, Guang Yao, Jianhua Xing, Attila Csikász-Nagy
2014 PLoS ONE  
For this purpose, we have previously developed a reverse engineering procedure to identify network topologies with high likelihood in generating desired systems properties.  ...  Our method searches the continuous parameter space of an assembly of network topologies, without enumerating individual network topologies separately as traditionally done in other reverse engineering  ...  The CPSS approach, by avoiding the enumeration of individual topologies for the search, further extends the application of this reverse engineering principle to biological networks containing large numbers  ... 
doi:10.1371/journal.pone.0105833 pmid:25170839 pmcid:PMC4149494 fatcat:6k6jiqxpc5a5laroyeqnfnklge

iMOT: an interactive package for the selection of spatially interacting motifs

A. Bhaduri, G. Pugalenthi, N. Gupta, R. Sowdhamini
2004 Nucleic Acids Research  
Interacting motifs have been shown to be useful in searching for distant homologues and establishing remote homologies among the largely unassigned sequences in genome databases.  ...  Information on such motifs should also be of value in protein folding, modelling and engineering experiments. The iMOT server can be accessed from  ...  We also thank NCBS (TIFR) for infrastructural support.  ... 
doi:10.1093/nar/gkh375 pmid:15215459 pmcid:PMC441513 fatcat:q7i3wp3m55chndu4mfxenajndi

SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs

S. Chakrabarti, A. P. Anand, N. Bhardwaj, G. Pugalenthi, R. Sowdhamini
2005 Nucleic Acids Research  
This paper reports SCANMOT, a web-based server that searches for similarities between proteins by simultaneous matching of multiple motifs.  ...  Motif-based search methods play a crucial role in establishing the connections between proteins that are particularly useful for distant relationships.  ...  We would also like to acknowledge the National Centre for Biological Sciences (TIFR) for financial and infrastructural support.  ... 
doi:10.1093/nar/gki493 pmid:15980468 pmcid:PMC1160253 fatcat:kkoszam64bfl7ninyjhu47hlza

ParSeq: searching motifs with structural and biochemical properties

M. Schmollinger, I. Fischer, C. Nerz, S. Pinkenburg, F. Gotz, M. Kaufmann, K.-J. Lange, R. Reuter, W. Rosenstiel, A. Zell
2004 Bioinformatics  
Searches for variable motifs such as proteinbinding sites or promoter regions are more complex than the search for casual motifs.  ...  Pure string matching programs are not able to find these motifs; hence, we developed ParSeq, a program that combines the search for motifs with certain structural properties, the verification of biochemical  ...  The usual batch approach to motif search assumes that the query motif is known. Hence, the task of the search engine is simply to find its occurrences in the sequences.  ... 
doi:10.1093/bioinformatics/bth083 pmid:14962930 fatcat:koodns63d5grth4om5ot6ruyqy
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