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Efficient algorithms for regular expression constrained sequence alignment

Yun-Sheng Chung, Chin Lung Lu, Chuan Yi Tang
2007 Information Processing Letters  
Due to this motivation, Arslan introduced the regular expression constrained sequence alignment problem and proposed an algorithm which, if implemented naïvely, can take time and space up to O(|Σ| 2 |V  ...  In an alignment of protein sequences it is natural to expect that functional motifs should be aligned together.  ...  To fulfill this need, Arslan introduced the regular expression constrained sequence alignment problem (RECSA, for short) [2] .  ... 
doi:10.1016/j.ipl.2007.04.007 fatcat:rjlypplyuvdojmgkr6vinvhjuy

Efficient Algorithms for Regular Expression Constrained Sequence Alignment [chapter]

Yun-Sheng Chung, Chin Lung Lu, Chuan Yi Tang
2006 Lecture Notes in Computer Science  
Due to this motivation, Arslan introduced the regular expression constrained sequence alignment problem and proposed an algorithm which, if implemented naïvely, can take time and space up to O(|Σ| 2 |V  ...  In an alignment of protein sequences it is natural to expect that functional motifs should be aligned together.  ...  To fulfill this need, Arslan introduced the regular expression constrained sequence alignment problem (RECSA, for short) [2] .  ... 
doi:10.1007/11780441_35 fatcat:7rm65zk5fnghdm4nuq3fxvmgme

An improved algorithm for the regular expression constrained multiple sequence alignment problem

Abdullah N. Arslan, Dan He
2006 Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06)  
We propose a new algorithm for the regular expression constrained multiple sequence alignment problem.  ...  The regular expression constrained sequence alignment has been introduced for this purpose.  ...  Our algorithm is more efficient than previously existing solutions for the regular expression constrained multiple sequence alignment problem.  ... 
doi:10.1109/bibe.2006.253324 dblp:conf/bibe/ArslanH06 fatcat:uvvti2zgx5d3nofmvk6v6tgana

RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints

Y.-S. Chung, W.-H. Lee, C. Y. Tang, C. L. Lu
2007 Nucleic Acids Research  
Funding to pay the Open Access publication charges for this article was provided by the ATU plan of MOE. Conflict of interest statement. None declared.  ...  ACKNOWLEDGEMENTS The authors thank the anonymous reviewers for their useful comments, which improved the usability of the web interface and the clarity of this article.  ...  METHODS The regular expression constrained sequence alignment problem was originally formulated by Arslan (23) . The algorithm proposed in (23) is for pairwise alignment with a single constraint.  ... 
doi:10.1093/nar/gkm275 pmid:17488842 pmcid:PMC1933182 fatcat:bw4minj3dbarflzf2yixq3mxny

Regular Language Constrained Sequence Alignment Revisited [chapter]

Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson
2011 Lecture Notes in Computer Science  
With this motivation, the Regular Expression Constrained Sequence Alignment Problem was introduced, which proposed an O(n 2 t 4 ) time and O(n 2 t 2 ) space algorithm for solving it, where n is the length  ...  In this article, we further speed up the algorithms for Regular Language Constrained Sequence Alignment by reducing their worst case time complexity bound to O(n 2 t 3 /log t).  ...  CONCLUSION We have revisited the problem of Regular Language Constrained Sequence Alignment with focus on improving the dense NFA case. While Chung et al.'  ... 
doi:10.1007/978-3-642-19222-7_39 fatcat:om3ifesp6zhbhapz2pq4tbpsnm

Regular Language Constrained Sequence Alignment Revisited

Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson
2011 Journal of Computational Biology  
With this motivation, the Regular Expression Constrained Sequence Alignment Problem was introduced, which proposed an O(n 2 t 4 ) time and O(n 2 t 2 ) space algorithm for solving it, where n is the length  ...  In this article, we further speed up the algorithms for Regular Language Constrained Sequence Alignment by reducing their worst case time complexity bound to O(n 2 t 3 /log t).  ...  CONCLUSION We have revisited the problem of Regular Language Constrained Sequence Alignment with focus on improving the dense NFA case. While Chung et al.'  ... 
doi:10.1089/cmb.2010.0291 pmid:21554020 fatcat:neinzhxdhzc2pibpbmjqfmuml4

Subject Index

2007 Journal of Discrete Algorithms  
Set Cover problems, 55 Regular expression Regular expression constrained sequence alignment, 647 Relaxing, zero-space A Zero-Space algorithm for Negative Cost Cycle Detection in net- works, 408  ...  alignment Regular expression constrained sequence alignment, 647 Sequence/structure alignments Fast detection of common sequence structure patterns in RNAs, 212 Shortest paths A Zero-Space algorithm  ... 
doi:10.1016/s1570-8667(07)00076-7 fatcat:wfqxglrznfb6do3wyittd5pfbi

SA-REPC – Sequence Alignment with Regular Expression Path Constraint [chapter]

Nimrod Milo, Tamar Pinhas, Michal Ziv-Ukelson
2010 Lecture Notes in Computer Science  
Our definition extends and generalizes the existing definitions of alignment-path constrained sequence alignments to the expressive power of regular expressions.  ...  In this paper, we define a novel variation on the constrained sequence alignment problem, the Sequence Alignment with Regular Expression Path Constraint problem, in which the constraint is given in the  ...  Acknowledgments The authors would like to thank Isana Vexler-Lublinsky for her helpful comments regarding microRNA target prediction and Dr. Chen Keasar for a helpful discussion.  ... 
doi:10.1007/978-3-642-13089-2_38 fatcat:jv25zrevefdpzbzavumrdvw4ni

CSA-X: Modularized Constrained Multiple Sequence Alignment [chapter]

T. M. Rezwanul Islam, Ian McQuillan
2017 Lecture Notes in Computer Science  
Hence, various constrained multiple sequence alignment (CMSA) algorithms have been developed in the literature, where researchers used anchor points, regular expressions, or context-free-grammars to specify  ...  We compare the accuracy of our program with another constrained multiple sequence alignment program called RE-MuSiC that similarly uses regular expressions for constraints.  ...  Constrained Multiple Sequence Alignment RECSA Aslan [5] proposed an algorithm RECSA (Regular Expression Constrained Sequence Alignment) for pairwise sequence alignment that accepts a single regular  ... 
doi:10.1007/978-3-319-58163-7_10 fatcat:34mloyszgffwxcpnsuz7ahqmh4

Scalable Convex Multiple Sequence Alignment via Entropy-Regularized Dual Decomposition

Jiong Zhang, Ian E H Yen, Pradeep Ravikumar, Inderjit S Dhillon
2017 Journal of machine learning research workshop and conference proceedings  
In this work, we propose an accelerated dual decomposition algorithm that exploits entropy regularization to induce closed-form solutions for each atomic-norm-constrained subproblem, giving a single-loop  ...  The proposed algorithm gives significantly better alignments than existing methods on sequences of length up to hundreds, where the existing convex programming method fails to converge in one day.  ...  It is easy to observe that given such two constrains, W can uniquely determine a consensus sequence z * and its alignment with all data sequences from , which is all we asked for in Star-alignment problem  ... 
pmid:28871272 pmcid:PMC5581665 fatcat:2pamqnmouzdjxhc56vxsumydwq

USAGE OF REGULAR EXPRESSIONS IN NLP

Gaganpreet Kaur .
2014 International Journal of Research in Engineering and Technology  
A usage of regular expressions to search text is well known and understood as a useful technique. Regular Expressions are generic representations for a string or a collection of strings.  ...  Regular expressions (regexps) are one of the most useful tools in computer science.  ...  The regular expression constrained sequence alignment has been introduced for this purpose.  ... 
doi:10.15623/ijret.2014.0301026 fatcat:mwd6trzphzd6bkodwjw4lmj7ay

Generalized Canonical Time Warping

Feng Zhou, Fernando De la Torre
2016 IEEE Transactions on Pattern Analysis and Machine Intelligence  
Unlike exact DTW that has quadratic complexity, we propose a linear time algorithm to minimize GCTW. (3) GCTW allows simultaneous alignment of multiple sequences.  ...  This paper presents generalized canonical time warping (GCTW), an extension of dynamic time warping (DTW) and canonical correlation analysis (CCA) for temporally aligning multi-modal sequences from multiple  ...  Fig. 9 . 9 Comparison of temporal alignment algorithms for aligning facial expression sequences between different people. (a) An example of two smiling expression sequences aligned by GCTW.  ... 
doi:10.1109/tpami.2015.2414429 pmid:26761734 fatcat:jbpz5wc65rdcjivrr3p5r2ss3u

Constrained sequence alignment: A general model and the hardness results

Yun-Sheng Chung, Chin Lung Lu, Chuan Yi Tang
2007 Discrete Applied Mathematics  
We give a polynomial time algorithm for pairwise constrained alignment for the generalized formulation, and prove the inapproximability of the problem when the number of sequences can be arbitrary.  ...  In this paper, a general model for constrained alignment is proposed so that analyses admitted are more flexible and that different pattern definitions can be treated in a simple unified way.  ...  Acknowledgment The authors would like to thank the anonymous reviewers for their useful comments which help to improve the clarity of this paper.  ... 
doi:10.1016/j.dam.2007.06.016 fatcat:jv37o5tcvfehrgoqav75wld2py

Detecting conserved secondary structures in RNA molecules using constrained structural alignment

Mugdha Khaladkar, Vandanaben Patel, Vivian Bellofatto, Jeffrey Wilusz, Jason T.L. Wang
2008 Computational biology and chemistry  
Constrained sequence alignment has been studied extensively in the past.  ...  In this paper, we present an efficient method for constrained structural alignment and apply the method to detecting conserved secondary structures, or structural motifs, in a set of RNA molecules.  ...  Acknowledgements We thank Marvin Nakayama, Bruce Shapiro and Bin Tian for helpful conversations during the preparation of this paper.  ... 
doi:10.1016/j.compbiolchem.2008.03.013 pmid:18472302 fatcat:v4l7j3dgb5e3rgbsj5wsl7k45m

The evolutionary computation approach to motif discovery in biological sequences

Michael A. Lones, Andy M. Tyrrell
2005 Proceedings of the 2005 workshops on Genetic and evolutionary computation - GECCO '05  
Particular attention is given to the problem of characterising regulatory DNA motifs and the value of expressive representations for providing accurate classification. * c ACM, 2005.  ...  It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in GECCO 2005 Workshop Proceedings, available from the ACM digital library.  ...  The authors wish to thank Finn Drabløs at NTNU for his contribution to the ideas developed in this paper.  ... 
doi:10.1145/1102256.1102258 dblp:conf/gecco/LonesT05 fatcat:lwlwl2cfabeazi7jpxnhzdki2q
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