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Subject Index

2005 Journal of Discrete Algorithms  
algorithms Constrained tree inclusion, 431 Comparative genomics Chaining algorithms for multiple genome compar- ison, 321 Comparison of sequences An improved algorithm for generalized compari- son  ...  Bafna and Pevzner Improving the algorithm of Bafna and Pevzner for the problem of sorting by transpositions: a prac- tical approach, 342 Alignment Decomposition algorithms for the tree edit dis- tance  ... 
doi:10.1016/s1570-8667(05)00042-0 fatcat:phytlwupp5hmtddg3ffue5546u

Subject Index

2007 Journal of Discrete Algorithms  
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  ...  the maximum clique in the visibility graph of a simple polygon, 524; Regular expression constrained sequence alignment, 647 Edit distance Efficient generation of super condensed neighborhoods, 501;  ... 
doi:10.1016/s1570-8667(07)00076-7 fatcat:wfqxglrznfb6do3wyittd5pfbi

A Parallel GPU-Designed Algorithm for the Constrained Multiple Sequence Alignment Problem [chapter]

Adam Gudyś, Sebastian Deorowicz
2011 Advances in Intelligent and Soft Computing  
As a result we propose a parallel version of Center-Star algorithm computing the constrained multiple sequence alignment at the GPU.  ...  One of the tasks of huge importance in bioinformatics is sequence alignment. We investigate its variant introduced a few years ago in which some additional requirement on the alignment is given.  ...  This work was partially supported by the European Community from the European Social Fund.  ... 
doi:10.1007/978-3-642-23169-8_39 dblp:conf/icmmi/GudysD11 fatcat:xsl23gkkjfhspjbfcnbos5bhpa

Subject Index

2004 Journal of Discrete Algorithms  
dynamic process graphs efficiently, 471 p-clustering problem Approximation algorithms for Hamming cluster- ing problems, 289 Parallel processing Approximating schedules for dynamic process graphs  ...  longest common subsequence problem for arc-annotated sequences, 257 Maximum independent set The longest common subsequence problem for arc-annotated sequences, 257 Median Budget constrained minimum  ... 
doi:10.1016/s1570-8667(04)00076-0 fatcat:3igwdxr5pba53eev4y6a2jzgie

DIALIGN P: fast pair-wise and multiple sequence alignment using parallel processors

Martin Schmollinger, Kay Nieselt, Michael Kaufmann, Burkhard Morgenstern
2004 BMC Bioinformatics  
(b) For alignments of large genomic sequences, we use a heuristics by splitting up sequences into sub-sequences based on a previously introduced anchored alignment procedure.  ...  Since alignments of different sequence pairs are completely independent of each other, they can be distributed to multiple processors without any effect on the resulting output alignments.  ...  Acknowledgements We would like to thank Michael Brudno for his help with CHAOS and Rasmus Steinkamp for installing our software at GOBICS. The work was partly supported by DFG grant MO 1048l1-1 to BM.  ... 
doi:10.1186/1471-2105-5-128 pmid:15357879 pmcid:PMC520757 fatcat:2eqeefrctzfmnpujvzjrhlehme

Shared Memory and Hardware Utilizations for the Parallelization of Local Sequences Alignment using SW Algorithm: A Review

Manhal ElfadilEltayeeb, Muhammad S. Abd Latiff, Ismail Fuzi Isnin
2015 International Journal of Computer Applications  
Many studies in recent years have focused on different implementations of Sequences Alignment Problems (SAP). However, researcher confused with the ambiguous classification of the SAP.  ...  It is becoming increasingly difficult to ignore the importance of aligning DNA and Protein sequences to infer properties of new sequences from well-known reference sequences established and sorted in genetics  ...  To develop parallel algorithms for sequences similarity problems, many considerations for designing parallel programs must be studied in essential and advanced stages to produce an efficient parallel application  ... 
doi:10.5120/20141-2257 fatcat:arg4ddbqsfbolbfdag6gwz75yy

Cache-Based Parallelization of Multiple Sequence Alignment Problem [chapter]

Gilles Parmentier, Denis Trystram, Jaroslaw Zola
2004 Lecture Notes in Computer Science  
In this paper we present new approach to the problem of parallel multiple sequence alignment.  ...  We describe an implementation based on the CaLi library, the software designed for caches implementation.  ...  Conclusions In this paper we have presented a new approach to the problem of parallel multiple sequence alignment.  ... 
doi:10.1007/978-3-540-27866-5_135 fatcat:76rnszyyhzet3gyihqd6sv2zhm

Parallel sequence alignment in limited space

J A Grice, R Hughey, D Speck
1995 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
While the innovative O(n2)-time and O(n)-space serial algorithm has been parallelized for multiple-instruction, multiple-data stream (MIMD) computers with only a communication-time slowdown, typically  ...  Unfortunately, the twin problem of sequence alignment, finding the optimal character-by-character correspondence between two sequences, is more complicated.  ...  Acknowledgments We especially thank Kevin Karplus for his many useful discussions and the anonymous reviewers for their helpful comments.  ... 
pmid:7584431 fatcat:vv6yu3eh55fvzij6e2sg2sqxcq

Constrained sequence alignment

K CHAO, R HARDISON, W MILLER
1993 Bulletin of Mathematical Biology  
Sequence Alignment The unfortunate scarcity of interaction between biologists and computer scientists is well illustrated by the parallel developments of dynamic-programming methods for comparing sequences  ...  It helps us to fish for related sequences in databanks, such as the GenBank database. It can also be used for the annotation of genomes. To be continued...  ...  Acknowledgements The work was partially done while the author was visiting the Institute for Mathematical  ... 
doi:10.1016/s0092-8240(05)80237-x fatcat:x3bi2kl6wncuxary4gnqrmavx4

Constrained sequence alignment

Kun-Mao Chao, Ross C. Hardison, Webb Miller
1993 Bulletin of Mathematical Biology  
Sequence Alignment The unfortunate scarcity of interaction between biologists and computer scientists is well illustrated by the parallel developments of dynamic-programming methods for comparing sequences  ...  It helps us to fish for related sequences in databanks, such as the GenBank database. It can also be used for the annotation of genomes. To be continued...  ...  Acknowledgements The work was partially done while the author was visiting the Institute for Mathematical  ... 
doi:10.1007/bf02460648 pmid:8298508 fatcat:sfmdcfabivbhpn7m37dsp3hol4

7. Combinatorial Parallel and Scientific Computing [chapter]

Ali Pınar, Bruce Hendrickson
2006 Parallel Processing for Scientific Computing  
But the relationship between parallel computing and discrete algorithms is much richer than the mere use of graph algorithms to support the parallelization of traditional scientific computations.  ...  New parallelization techniques for combinatorial algorithms need to be developed to support these nontraditional scientific approaches.  ...  Multiple alignment of the sequences of hundreds of bacterial genomes is a computational problem that can be attempted only with a new suite of efficient alignment algorithms on parallel computers.  ... 
doi:10.1137/1.9780898718133.ch7 fatcat:szr5t7calne2fbhkbkvwccrj6y

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay
2015 PeerJ  
With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings.  ...  When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected  ...  ACKNOWLEDGEMENTS We are grateful to David Luebke and Cliff Wooley of NVidia Corporation for their help in understanding some of the nuances of NVidia GPU programming.  ... 
doi:10.7717/peerj.808 pmid:25780763 pmcid:PMC4358639 fatcat:jxjlbuw6drahvgvsuuxueopfcm

Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space [article]

Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J Wheelan, Steven Salzberg, Alex Szalay
2014 bioRxiv   pre-print
Motivation: In computing pairwise alignments of biological sequences, software implementations employ a variety of heuristics that decrease the computational effort involved in computing potential alignments  ...  Results: We implemented a read aligner called A21 that exploits GPU-based parallel sort and reduction techniques to restrict the number of locations where potential alignments may be found.  ...  ACKNOWLEDGEMENTS We are grateful to David Luebke and Cliff Wooley of NVidia Corporation for their help in understanding some of the nuances of NVidia GPU hardware.  ... 
doi:10.1101/007641 fatcat:7oxca2pcmffn7jy7b4woqhraiq

ACCELERATE MULTIPLE SEQUENCE ALIGNMENT BY CLUSTER ALGORITHM USING RECONFIGURABLE HARDWARE

Asmaa Seliem, Hesham A.Hamed, Wael AbouElWafa
2020 Journal of Al-Azhar University Engineering Sector  
A hardware-based multiple sequence alignment architecture is described in this manuscript, expresses a comprehensive blueprint of the hardware implementation of small sequence alignment, for pair-wise  ...  As a conclusion for this procedure, the whole human genome multiple sequencing alignment of K-Mer length can be done in less than one hour, to achieve a local hardware sequence alignment in every bioinformatics  ...  problem; therefore, there is no efficient algorithm to solve it. • Heuristic algorithms have been proposed to align multiple sequences.  ... 
doi:10.21608/auej.2020.103817 fatcat:gju6gmrlv5ej3apzyooqujxg6m

Genome Sequence Analysis: A Survey

Hassan Mathkour, Muneer Ahmad
2009 Journal of Computer Science  
Approach: This study described the concepts, tools, methodologies, algorithms being used for sequence analysis.  ...  The similarity and alignments concepts can not be addressed directly with one technique or algorithm, a better performance was achieved by the comprehension of different concepts.  ...  Arslan [11] described an improved algorithm for multiple sequence alignment problem, this approach considers two layers each of which corresponds to part of the dynamic programming matrix for the alignment  ... 
doi:10.3844/jcssp.2009.651.660 fatcat:47vacjbgjzcixgfqjf5xjf4jbq
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