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A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

Sean R Eddy
<span title="2002-07-02">2002</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The dynamic programming algorithm for aligning a CM to an RNA sequence of length N is O(N3) in memory. This is only practical for small RNAs.  ...  I describe a divide and conquer variant of the alignment algorithm that is analogous to memory-efficient Myers/Miller dynamic programming algorithms for linear sequence alignment.  ...  I also wish to thank Elena Rivas and Robin Dowell for critical comments on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12095421">pmid:12095421</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC119854/">pmcid:PMC119854</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j4zsregp5fgtzn4xbfyjcdya3a">fatcat:j4zsregp5fgtzn4xbfyjcdya3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200711004406/https://link.springer.com/content/pdf/10.1186%2F1471-2105-3-18.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/af/80/af80e696dfbb83d072e15f16e053735ebf74e64d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC119854" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Survey of Compute Intensive Algorithms for Ribo Nucleic Acids Structural Detection

Ra`ed M. Al-Khatib, Rosni Abdullah, Nur`Aini Abdul Rash
<span title="2009-10-01">2009</span> <i title="Science Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wake4w3hqzd4ndiy2zowpciv64" style="color: black;">Journal of Computer Science</a> </i> &nbsp;
Results: Our findings of this survey confirmed that Dynamic Programming (DP) method via CMP algorithms can be used to predict the RNA secondary structure with simple PK and it gives good results.  ...  Our contribution in this article was a comprehensive survey of methods for solving RNA secondary structure prediction with Pseudoknots (PK) and sequence alignment in bioinformatics.  ...  DP Algorithm. 5 DP Solution for large A memory-efficient dynamic -O(n 2 log n) A DP Solution to the RNA-SP RNA-SP by using programming algorithm for optimal problem for a large by using divide and conquer  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3844/jcssp.2009.680.689">doi:10.3844/jcssp.2009.680.689</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3nnefutdhvg5xmenpx6frv3zei">fatcat:3nnefutdhvg5xmenpx6frv3zei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110108183536/http://www.scipub.org/fulltext/jcs/jcs510680-689.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/46/60/46606447906766b643a7f4d6e1b24cc6d15df696.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3844/jcssp.2009.680.689"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Exploiting Parallelization for RNA Secondary Structure Prediction in Cluster [chapter]

Guangming Tan, Shengzhong Feng, Ninghui Sun
<span title="">2005</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
A popular dynamic programming (DP) algorithm uses a stochastic context-free grammar to model RNA secondary structures, its time complexity is O(N 4 ) and spatial complexity is O(N 3 ).  ...  Many computational methods have been proposed in an attempt to predict RNA secondary structures.  ...  In this paper, we present an efficient parallel algorithm for aligning an RNA sequence to an SCFG model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11428862_152">doi:10.1007/11428862_152</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/27cih3u67faddbro5mw2f6s5mq">fatcat:27cih3u67faddbro5mw2f6s5mq</a> </span>
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Memory efficient alignment between RNA sequences and stochastic grammar models of pseudoknots

Yinglei Song, Chunmei Liu, Russell L. Malmberg, Congzhou He, Liming Cai
<span title="">2006</span> <i title="Inderscience Publishers"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qozp5qsymng6nkr5dpjrxwfwxq" style="color: black;">International Journal of Bioinformatics Research and Applications</a> </i> &nbsp;
In this paper, we develop a memory efficient algorithm for sequence-structure alignments including pseudoknots.  ...  ., 2003) in Stochastic Parallel Communicating Grammar Systems (SPCGS) has extended SCFG to model RNA pseudoknots. However, the alignment algorithm requires O(n 4 ) memory for a sequence of length n.  ...  A dynamic programming algorithm has been designed for finding the optimal alignment between a given RNA and a SPCGS model, similar to the CYK algorithm designed for optimising the statistical alignment  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1504/ijbra.2006.010606">doi:10.1504/ijbra.2006.010606</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18048167">pmid:18048167</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ggxwyhsghrbrvotlzhbmpo4tty">fatcat:ggxwyhsghrbrvotlzhbmpo4tty</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922014433/http://cobweb.cs.uga.edu/~cai/papers/2006IJBRA.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b1/42/b142d074ff566c4c8e09d3de8de351568f9f5ab4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1504/ijbra.2006.010606"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

Timo Lassmann, Oliver Frings, Erik L. L. Sonnhammer
<span title="2008-12-22">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences.  ...  Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure.  ...  Combining Kalign2 with additional annotations like predicted secondary structure for RNA constitutes an easy but powerful way to enhance alignment accuracy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn1006">doi:10.1093/nar/gkn1006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19103665">pmid:19103665</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2647288/">pmcid:PMC2647288</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lul4phleqvct3idwkserysojam">fatcat:lul4phleqvct3idwkserysojam</a> </span>
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A MEMORY EFFICIENT ALGORITHM FOR STRUCTURAL ALIGNMENT OF RNAs WITH EMBEDDED SIMPLE PSEUDOKNOTS

THOMAS WONG, Y. S. CHIU, TAK-WAH LAM, S. M. YIU
<span title="">2007</span> <i title="PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO."> Proceedings of the 6th Asia-Pacific Bioinformatics Conference </i> &nbsp;
In this paper, we consider the problem of structural alignment of a target RNA sequence of length n and a query RNA sequence of length m with known secondary structure that may contain embedded simple  ...  We propose a memory efficient algorithm to solve the same problem. We reduce the space complexity to O(mn2 + n3) while maintaining the same time complexity of Dost et al.'s algorithm.  ...  By restricting their supporting structure to be a subset of the structures having 2-crossing properties, their dynamic programming algorithm runs faster and uses less memory with time complexity of O(mn  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9781848161092_0012">doi:10.1142/9781848161092_0012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/76xj56iwfjacbgnrdylwyqkg3i">fatcat:76xj56iwfjacbgnrdylwyqkg3i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705101737/http://www.comp.nus.edu.sg/%7Ewongls/psZ/apbc2008/apbc105a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/88/da/88daed153141468b80036aa717a03827ee2b2629.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1142/9781848161092_0012"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> worldscientific.com </button> </a>

GPU Parallelization of Algebraic Dynamic Programming [chapter]

Peter Steffen, Robert Giegerich, Mathieu Giraud
<span title="">2010</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Algebraic Dynamic Programming (ADP) is a framework to encode a broad range of optimization problems, including common bioinformatics problems like RNA folding or pairwise sequence alignment.  ...  In all these optimization problems, the logical problem decomposition follows the decomposition of the input sequence  ...  Acknowledgements Part of this research was done during P. Steffen's stay in Université Lille 1. This research was carried through the "NVIDIA Professor Partnership" program.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-14403-5_31">doi:10.1007/978-3-642-14403-5_31</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dnrrorltljgmddh37md5vj3no4">fatcat:dnrrorltljgmddh37md5vj3no4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110524234639/http://hal.archives-ouvertes.fr/docs/00/43/82/19/PDF/CP54.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/48/66/48669f8254f12d0695ec02afa2f1942fd91b209a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-14403-5_31"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

RAGA: RNA sequence alignment by genetic algorithm

C Notredame
<span title="1997-11-15">1997</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
We describe a new approach for accurately aligning two homologous RNA sequences when the secondary structure of one of them is known.  ...  This method allows us to optimize an objective function that describes the quality of a RNA pairwise alignment, taking into account both primary and secondary structure, including pseudoknots.  ...  ACKNOWLEDGEMENTS This work was partly supported by a grant from the EC Biotechnology Program (BIO4-CT95 0130). We wish to thank Burkhart Rost and Miguel Andrade for useful comments.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/25.22.4570">doi:10.1093/nar/25.22.4570</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9358168">pmid:9358168</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC147093/">pmcid:PMC147093</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yze3xxoeajh27f2wz2gsnl5z6i">fatcat:yze3xxoeajh27f2wz2gsnl5z6i</a> </span>
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An experimental study of optimizing bioinformatics applications

Guangming Tan, Lin Xu, Shengzhong Feng, Ninghui Sun
<span title="">2006</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t3x4vqewrncrfgn2wu7cafsbsq" style="color: black;">Proceedings 20th IEEE International Parallel &amp; Distributed Processing Symposium</a> </i> &nbsp;
, we overlap computation with I/O to produce an improved high-throughput algorithm with reduced time and memory requirements. 2) For a CPU-intensive RNA secondary structure prediction algorithm, we propose  ...  Based on the computational behavior of these bioinformatics applications, we propose two optimized algorithms on high performance computer architectures. 1) For the data(I/O) intensive program, MegaBlast  ...  structure of an RNA sequence is a nested dynamic programming.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ipdps.2006.1639541">doi:10.1109/ipdps.2006.1639541</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ipps/TanXFS06.html">dblp:conf/ipps/TanXFS06</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wp3kkwk3kneznacbuybtouubz4">fatcat:wp3kkwk3kneznacbuybtouubz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130811193230/http://bioperf.org/TXF06.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c5/83/c583c1b21af1812a74be8019fd3f9c62a1bfd3ec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ipdps.2006.1639541"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Structural Alignment of Two RNA Sequences with Lagrangian Relaxation [chapter]

Markus Bauer, Gunnar W. Klau
<span title="">2004</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In this paper we address the problem of optimally aligning two given RNA sequences either with or without known structure (allowing for pseudoknots).  ...  Traditional alignment algorithms can only account for the sequence of bases, but not for the base pairings.  ...  [11] presented a Branch-and-Cut algorithm for aligning an RNA molecule of known sequence and known structure to an RNA molecule of known sequence but unknown structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-30551-4_12">doi:10.1007/978-3-540-30551-4_12</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bhylncq5uvhuroopfdgtzip6ki">fatcat:bhylncq5uvhuroopfdgtzip6ki</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060211223447/http://www.ads.tuwien.ac.at:80/people/gunnar/pubs/bk-satrslr-04.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5f/fb/5ffb226d4389fa5358d5b6d2e22650512b3836c3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-30551-4_12"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Finding Common RNA Secondary Structures: A Case Study on the Dynamic Parallelization of a Data-driven Recurrence

Steven T. Stewart, Eric Aubanel, Patricia A. Evans
<span title="">2012</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t3x4vqewrncrfgn2wu7cafsbsq" style="color: black;">2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops &amp; PhD Forum</a> </i> &nbsp;
This paper presents the dynamic parallelization of a sequential algorithm for finding common RNA secondary structures that initially does not appear to be amenable to parallelization.  ...  Our results also show the usefulness of combining both bottom-up and top-down perspectives when designing a parallel dynamic programming algorithm.  ...  Figure 2 . 2 Dynamic programming formulation for finding common RNA secondary structures. Figure 3 . 3 Dependency graph for the sequence (upper-left) aligned with itself.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ipdpsw.2012.89">doi:10.1109/ipdpsw.2012.89</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ipps/StewartAE12.html">dblp:conf/ipps/StewartAE12</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ubyrl7czdjgmpgeparugcsu5by">fatcat:ubyrl7czdjgmpgeparugcsu5by</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170705121239/http://www.hicomb.org/HiCOMB2005/papers/HICOMB2012-07.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/91/cb/91cb2bc3290425a14b95dedeffa357bc9af6aeee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ipdpsw.2012.89"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Cache-Oblivious Dynamic Programming for Bioinformatics

Rezaul Alan Chowdhury, Hai-Son Le, Vijaya Ramachandran
<span title="">2010</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q75ftrlivrhrnno5ijjuyufx5a" style="color: black;">IEEE/ACM Transactions on Computational Biology &amp; Bioinformatics</a> </i> &nbsp;
Index Terms-sequence alignment, median, RNA secondary structure prediction, dynamic programming, cache-efficient, cache-oblivious.  ...  We present efficient cache-oblivious algorithms for some well-studied string problems in bioinformatics including the longest common subsequence, global pairwise sequence alignment and 3-way sequence alignment  ...  ACKNOWLEDGMENT We thank Mike Brudno for the CFTR DNA sequences, Robin Gutell for the rRNA sequences, and David Zhao for the MED-Knudsen, MED-ukk.alloc and MED-ukk.checkp code.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2008.94">doi:10.1109/tcbb.2008.94</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20671320">pmid:20671320</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vn2vc4qlqnervbqj3veiyt36e4">fatcat:vn2vc4qlqnervbqj3veiyt36e4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20110401090229/http://www.cs.utexas.edu/~shaikat/papers/bio-dp.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/86/c9/86c9b7b093210f8435cbc66dd6b0b16df570af59.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2008.94"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Tree decomposition based fast search of RNA structures including pseudoknots in genomes

Y. Song, C. Liu, R. Malmberg, F. Pan, L. Cai
<span title="">2005</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vt2vr2w2rfdp5gft37lygug6ha" style="color: black;">2005 IEEE Computational Systems Bioinformatics Conference (CSB&#39;05)</a> </i> &nbsp;
However, due to the lack of efficient algorithms for accurate RNA structuresequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not  ...  Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic  ...  Acknowledgments We would like to thank the anonymous reviewers for their constructive remarks on an earlier version of this paper.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/csb.2005.52">doi:10.1109/csb.2005.52</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/csb/SongLMPC05.html">dblp:conf/csb/SongLMPC05</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gslkicpyeva5tnehygcp25qxuu">fatcat:gslkicpyeva5tnehygcp25qxuu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811193050/http://cobweb.cs.uga.edu/~cai/papers/2005CSB.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0b/01/0b01a059622dfa4b5b52a830c1305a5df2ee754c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/csb.2005.52"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Comppsa: A Component-Based Pairwise Rna Secondary Structure Alignment Algorithm

Ghada Badr, Arwa Alturki
<span title="2017-06-04">2017</span> <i title="Zenodo"> Zenodo </i> &nbsp;
Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment.  ...  The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures.  ...  For the primary structure, the sequence of the RNA is aligned, while for secondary structure, the RNA structure is aligned.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1340239">doi:10.5281/zenodo.1340239</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4zz3ax6zjzbohlwjyfpcyu5kkq">fatcat:4zz3ax6zjzbohlwjyfpcyu5kkq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200224133236/https://zenodo.org/record/1340240/files/10007311.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/53/ac53de685e9be086de349fee89a4802306732a6b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1340239"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

How do RNA folding algorithms work?

Sean R Eddy
<span title="">2004</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t2bqrmk7orfmxpqzqwiiyjwide" style="color: black;">Nature Biotechnology</a> </i> &nbsp;
definition of the best score for a sub-sequence i,j looks at four possibilities: Figure 1 1 Dynamic programming algorithm for RNA secondary structure prediction.  ...  Storing the S(i,j) matrix requires memory proportional to N 2 , similar to what sequence alignment algorithms need.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt1104-1457">doi:10.1038/nbt1104-1457</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15529172">pmid:15529172</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/siabhsaaiffbvczclmfdygg7m4">fatcat:siabhsaaiffbvczclmfdygg7m4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170315113802/http://cs.utsa.edu:80/~jruan/teaching/cs5263_fall_2007/papers/how_to_predict_rna_structure.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/93/6d/936dfe04f6f7c8c3f4e16555a124561812806cc3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt1104-1457"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>
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