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Linear-Time Protein 3-D Structure Searching with Insertions and Deletions [chapter]

Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane
2009 Lecture Notes in Computer Science  
., insertions and deletions).  ...  It becomes more and more important to search for similar structures from molecular 3-D structure databases in the structural biology of the post genomic era.  ...  Jesper Jansson was supported by the Special Coordination Funds for Promoting Science and Technology.  ... 
doi:10.1007/978-3-642-04241-6_26 fatcat:q7qsbzy5kbh7fdex6tt5iwaufe

Linear-time protein 3-D structure searching with insertions and deletions

Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane
2010 Algorithms for Molecular Biology  
., insertions and deletions).  ...  It becomes more and more important to search for similar structures from molecular 3-D structure databases in the structural biology of the post genomic era.  ...  Jesper Jansson was supported by the Special Coordination Funds for Promoting Science and Technology.  ... 
doi:10.1186/1748-7188-5-7 pmid:20047663 pmcid:PMC2830924 fatcat:vdudzahft5htjmvvnfn4zxhrby

A Genetic Algorithms Approach to Non-coding RNA Gene Searches

S. Smith
2006 2006 IEEE Mountain Workshop on Adaptive and Learning Systems  
A search space with many local minima makes gradient decent an unattractive alternative.  ...  It is shown that a fixed-length representation for alignment of two sequences taken from the protein threading literature can be adapted for use with covariance models.  ...  The internal structure of the nodes which handles insertions and deletions relative to the consensus structure is described in Subsection B below.  ... 
doi:10.1109/smcals.2006.250691 fatcat:tfeh6g6jr5bsdpwggng3uxle5q

Querying Pathways in Protein Interaction Networks Based on Hidden Markov Models

Xiaoning Qian, Sing-Hoi Sze, Byung-Jun Yoon
2009 Journal of Computational Biology  
This enables the search for very long paths with more than 10 proteins within a few minutes on a desktop computer.  ...  Given a query path, our method identifies the top k matching paths in the network, which may contain any number of consecutive insertions and deletions.  ...  Note that this is about 25 .D D k/ times larger compared to the previous running time (3 min.), which confirms that the computational complexity is also linear in the maximum number of insertions D and  ... 
doi:10.1089/cmb.2008.02tt pmid:19193142 pmcid:PMC3203511 fatcat:hi2lnseoivhqdawi7kdjt4jthe


Kyle Ellrott, Jun-tao Guo, Victor Olman, Ying Xu
2007 Computational Systems Bioinformatics  
the protein structure.  ...  We have analyzed the alignment patterns for homologous and analogous sequences to determine patterns of insertion and deletions, and used that information to determine the statistics of insertions and  ...  ACKNOWLEDGMENTS The work is, in part, supported by National Science Foundation (DBI-0354771/ITR-IIS-0407204/CCF-0621700), and a Distinguished Cancer Scholar grant from the Georgia Cancer Coalition.  ... 
doi:10.1142/9781860948732_0034 fatcat:67nfl6acnzgrxdaqwo4i2qpwmy

Some Results for Elementary Operations [chapter]

Athanasios K. Tsakalidis
2009 Lecture Notes in Computer Science  
We present a number of results for elementary operations concerning the areas of data structures, computational geometry, graph algorithms and string algorithms.  ...  , rectangle enclosure, dominance searching, intersection queries, hidden line elimination and string manipulation.  ...  Acknowledgement We have presented some results derived since 1983 in collaboration with my students, my colleagues and my advisor Kurt Mehlhorn. I met Kurt in 1976.  ... 
doi:10.1007/978-3-642-03456-5_8 fatcat:dtpunwag2rdzzmbsryzuzflibq

QNet: A Tool for Querying Protein Interaction Networks

Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan
2008 Journal of Computational Biology  
We show that QNet searches queries with up to 9 proteins in seconds on current networks, and outperforms sequence-based searches.  ...  In simulations, we show that QNet can handle queries of up to 9 proteins in seconds in a network with about 5,000 vertices and 15,000 interactions, and that it outperforms sequence-based searches.  ...  B.D. and V.B. were supported in part by the NSF grant CCF-0425926, T.S. was supported by the Tauber fund, and R.S. was supported by an Alon fellowship.  ... 
doi:10.1089/cmb.2007.0172 pmid:18707533 fatcat:pi5br7dp75gbxcm4qmlm5aey6e

Learning Models for Aligning Protein Sequences with Predicted Secondary Structure [chapter]

Eagu Kim, Travis Wheeler, John Kececioglu
2009 Lecture Notes in Computer Science  
We introduce several new models for scoring alignments of protein sequences with predicted secondary structure, which use the predictions and their confidences to modify both the substitution and gap cost  ...  Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted secondary structure.  ...  Acknowledgements We thank Matt Cordes and Chuong Do for helpful discussions, and the reviewers for their suggestions.  ... 
doi:10.1007/978-3-642-02008-7_36 fatcat:bnpnmye4nfcw7ctebwuloai5pi

Detecting distant homologs using phylogenetic tree-based HMMs

Bin Qian, Richard A. Goldstein
2003 Proteins: Structure, Function, and Bioinformatics  
With these common features, we can search the biological database and find new homologous sequences.  ...  Proteins 2003;52:446 -453.  ...  ACKNOWLEDGMENTS We thank Sarah Ingalls, Feng Gao, Matt Dimmic, David States, and Tom Blackwell for helpful discussions, and Todd Raeker and Michael Kitson for computational assistance.  ... 
doi:10.1002/prot.10373 pmid:12866055 fatcat:5e7rjztb5rccrguiku6twp335q

Phase-concurrent hash tables for determinism

Julian Shun, Guy E. Blelloch
2014 Proceedings of the 26th ACM symposium on Parallelism in algorithms and architectures - SPAA '14  
Compared to standard sequential linear probing, we get up to 52 times speedup on 40 cores with dual hyperthreading.  ...  We also show that the cost of insertions and deletions for our deterministic hash table is only slightly more expensive than for a non-deterministic version that we implemented.  ...  We thank Kristy Gardner and Phillip Gibbons for useful discussions.  ... 
doi:10.1145/2612669.2612687 dblp:conf/spaa/ShunB14 fatcat:ywjhokjs6zd3rllzk5uiive6b4

Aligning Protein Sequences with Predicted Secondary Structure

John Kececioglu, Eagu Kim, Travis Wheeler
2010 Journal of Computational Biology  
We make several advances in alignment of protein sequences annotated with predicted secondary structure: (1) more accurate models for scoring alignments, (2) efficient algorithms for optimal alignment  ...  More specifically, the new models use secondary structure predictions and their confidences to modify the scoring of both substitutions and gaps.  ...  ACKNOWLEDGMENTS We thank Matt Cordes and Chuong Do for helpful discussions, and the reviewers for their suggestions. This research was supported by the U.S.  ... 
doi:10.1089/cmb.2009.0222 pmid:20377464 fatcat:herkjbxewrfrrml3vqa5lowcq4

Fast Search of Sequences with Complex Symbol Correlations using Profile Context-Sensitive HMMS and Pre-Screening Filters

Byung-Jun Yoon, P. P. Vaidyanathan
2007 2007 IEEE International Conference on Acoustics, Speech and Signal Processing - ICASSP '07  
Experimental results show that the proposed approach can make the search speed eighty times faster.  ...  However, a profile-csHMM based search is quite slow, hence not practical for searching a large database.  ...  Modeling insertions and deletions In order to allow additional insertions and deletions in the original alignment, we add insert states I k and delete states D k to the ungapped model that has been obtained  ... 
doi:10.1109/icassp.2007.366687 dblp:conf/icassp/YoonV07 fatcat:xkobeanipbh4bmufqlr3kz64re

Efficient sequence alignment algorithms

Michael S. Waterman
1984 Journal of Theoretical Biology  
Multiple insertionJdeletions are known to increase computation time from O( n 2 ) to O ( n 3 ) although Gotoh has presented an O(n2) algorithm in the case the multiple insertion/deletion weighting function  ...  Fitch and Smith have recently given an example where multiple insertion/deletions (rather than a series of adjacent single insertion/deletions) are necessary to achieve the correct alignment.  ...  protein sequences, and they determined that a specific range of weights for multiple insertion/deletions were necessary to obtain correct alignments.  ... 
doi:10.1016/s0022-5193(84)80037-5 pmid:6748696 fatcat:ie4j2pbj5vhibfnalj264bdm64

Application Bat Algorithm for Estimating Super Pairwise Alignment Parameters on Similarity Analysis Between Virus Protein Sequences

Dinita Rahmalia, Teguh Herlambang
2021 Jurnal Ilmiah Teknik Elektro Komputer dan Informatika  
D is the search space dimension.  ...  If 0 k l  , it is the type III mutation and if 0 k l  , it is the type IV mutation. || k l is the length of the deleted or inserted segment [3] .  ...  sequences (Dinita Rahmalia) wavelength, a fixed frequency, and loudness for searching prey.  ... 
doi:10.26555/jiteki.v6i2.14323 fatcat:v2pmhjqmwnedlncoeaev63hk3i

Lysogenic conversion of staphylococcal lipase is caused by insertion of the bacteriophage L54a genome into the lipase structural gene

C Y Lee, J J Iandolo
1986 Journal of Bacteriology  
This is due to the insertion of bacteriophage L54a DNA into the geh structural gene. The nucleotide sequence of this 2,968-base-pair DNA fragment was determined.  ...  Thus, L54a inserted into the structural gene of lipase near the carboxyl end of the protein between amino acids 635 and 664.  ...  Deletions of 80 (A), 170 (B), 270 (C), and 360 (D) bp from the right end of the ClaI D fragment were used. In each panel, lanes 1 and 3 are digested chromosomal DNA of strain PS54.  ... 
doi:10.1128/jb.166.2.385-391.1986 pmid:3009394 pmcid:PMC214616 fatcat:z54bxu5gtzdnhb7g55h2iogdyq
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