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CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment

Xi Chen, Chen Wang, Shanjiang Tang, Ce Yu, Quan Zou
2017 BMC Bioinformatics  
The multiple sequence alignment (MSA) is a classic and powerful technique for sequence analysis in bioinformatics.  ...  Second, the center star strategy is suited for aligning similar sequences. But its first stage, center sequence selection, is highly time-consuming and requires further optimization.  ...  Acknowledgements We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Tesla K40 GPU used for this research.  ... 
doi:10.1186/s12859-017-1725-6 pmid:28646874 pmcid:PMC5483318 fatcat:76t4qv5cancdxi352xqhlncvh4

3D-stacked many-core architecture for biological sequence analysis problems

Pei Liu, Ahmed Hemani, Kolin Paul
2015 2015 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS)  
, including pairwise sequence alignment, multiple sequence alignment, database search, and short read sequence mappings.  ...  By exploiting the compute intensive execution stages of popular sequence analysis applications, we present and evaluate a VLSI architecture with a focus on those that target at biological sequences directly  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1109/samos.2015.7363678 dblp:conf/samos/LiuHP15 fatcat:xysaiokksbem7cqlnvpqahr7be

3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems

Pei Liu, Ahmed Hemani, Kolin Paul, Christian Weis, Matthias Jung, Norbert Wehn
2017 International journal of parallel programming  
, including pairwise sequence alignment, multiple sequence alignment, database search, and short read sequence mappings.  ...  By exploiting the compute intensive execution stages of popular sequence analysis applications, we present and evaluate a VLSI architecture with a focus on those that target at biological sequences directly  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s10766-017-0495-0 fatcat:eftphbiuojastkml73s6rmik2u

GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data

Nauman Ahmed, Jonathan Lévy, Shanshan Ren, Hamid Mushtaq, Koen Bertels, Zaid Al-Ars
2019 BMC Bioinformatics  
Pairwise sequence alignment can be performed with and without traceback.  ...  In this article we present GASAL2, a GPU library for aligning DNA and RNA sequences that outperforms existing CPU and GPU libraries.  ...  Conclusions In this paper, we presented GASAL2, a high performance and GPU accelerated library, for pairwise sequence alignment of DNA and RNA sequences.  ... 
doi:10.1186/s12859-019-3086-9 fatcat:pol35timxzdpbea3pclozsts74

Short Read Mapping: An Algorithmic Tour

Stefan Canzar, Steven L. Salzberg
2017 Proceedings of the IEEE  
The advent of ultra-high-throughput next-generation sequencing (NGS) technology in 2007 presented major new challenges for alignment.  ...  Read lengths subsequently increased, and have now reached 150 bp in the highest throughput sequencing machines.  ...  Acknowledgments This work was supported in part by the U.S. National Institutes of Health under grant R01 HG006102 to SLS. Stefan Canzar received his Diploma in Computer  ... 
doi:10.1109/jproc.2015.2455551 pmid:28502990 pmcid:PMC5425171 fatcat:ic6d6z5ggbazdkaotcotdtbo3u

Energy efficiency of sequence alignment tools—Software and hardware perspectives

Michał Kierzynka, Lars Kosmann, Micha vor dem Berge, Stefan Krupop, Jens Hagemeyer, René Griessl, Meysam Peykanu, Ariel Oleksiak
2017 Future generations computer systems  
We compare the energy efficiency of the most established software tools performing exact pairwise sequence alignment on various computational architectures: CPU, GPU and Intel Xeon Phi.  ...  Pairwise sequence alignment is ubiquitous in modern bioinformatics.  ...  The software implements a semi-global version of the Needleman-Wunsch algorithm and uses multiple GPUs to compute the score and shift for each selected pair of sequences.  ... 
doi:10.1016/j.future.2016.05.006 fatcat:3kejmtmjwbfvlcmlk7fclqwl7q

Pairwise heuristic sequence alignment algorithm based on deep reinforcement learning [article]

Yong Joon Song, Dong Jin Ji, Hye In Seo, Gyu Bum Han, Dong Ho Cho
2020 arXiv   pre-print
Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes.  ...  However, the traditional sequence alignment method is considerably complicated in proportion to the sequences' length, and it is significantly challenging to align long sequences such as a human genome  ...  Also, if we separate these two paths into two segments, the first segment can be seen as a small sequence alignment in the block with m 1 × (m 1 + m 3 ) subsequences, and the shared remaining paths, m  ... 
arXiv:2010.13478v1 fatcat:kyuvdk2irbe5xdyi3cwozjuxdy

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  ...  The score in each cell represents the maximum score for the alignment of any length ending at specific cell. Optimal alignment is then the highest scoring of the matrix.  ... 
doi:10.5120/20141-2257 fatcat:arg4ddbqsfbolbfdag6gwz75yy

An algorithm for fast edit distance computation on GPUs

Reza Farivar, Harshit Kharbanda, Shivaram Venkataraman, Roy H. Campbell
2012 2012 Innovative Parallel Computing (InPar)  
, security kernels, natural language translation and genome sequence alignment.  ...  The problem of finding the edit distance between two sequences (and its closely related problem of longest common subsequence) are important problems with applications in many domains like virus scanners  ...  Pairwise alignment in a larger context Pairwise alignment can be used to compute the edit distance between two sequences and then align these sequences with an allowed fixed number of insertions, deletions  ... 
doi:10.1109/inpar.2012.6339593 fatcat:a46yelyucranxmydnw6pykoklu

Chapter 3: Mining Genomic Sequence Data for Related Sequences Using Pairwise Statistical Significance [chapter]

Yuhong Zhang, Yunbo Rao
2013 Science, Engineering, and Biology Informatics  
However, it is both computationally and data intensive. To prevent it from becoming a performance bottleneck, we resort to high performance computation techniques for accelerating the computation.  ...  Almost everything in bioinformatics depends on the inter-relationship between sequence, structure and function (all encapsulated in the term relatedness), which is far from being well understood.  ...  Waterman and Vingron 46 showed that, for protein sequences, the estimation results using sequences selected from databases are in good agreement with those using random sequence models with independent  ... 
doi:10.1142/9789814551014_0003 fatcat:bvtae7xtnfclzeqffplqy2tmqu

Computer Architecture-Aware Optimisation of DNA Analysis Systems [article]

Hasindu Gamaarachchi
2021 arXiv   pre-print
The cost of sequencing a human genome also has reduced from billions of dollars to hundreds of dollars.  ...  Consequently, the full utility of an ultra-portable sequencer for sequencing in-the-field or at the point-of-care is limited by the lack of portable lightweight analytic techniques.  ...  Sequence aligners only perform pairwise alignment between an individual read and the reference genome.  ... 
arXiv:2101.05012v1 fatcat:wcujdqliwzgrxd2zc2wcudbqpu

Parallel computing for genome sequence processing

You Zou, Yuejie Zhu, Yaohang Li, Fang-Xiang Wu, Jianxin Wang
2021 Briefings in Bioinformatics  
Then, the parallel computing for genome sequence processing is discussed with four common applications: genome sequence alignment, single nucleotide polymorphism calling, genome sequence preprocessing,  ...  The programming model of each hardware and application provides a reference for researchers to choose high-performance computing tools.  ...  Funding This work is supported in part by the National Natural Science Foundation of China under grants (Nos U1909208, 61732009, 61772557), Hunan Provincial Science and Technology Program (No. 2018WK4001  ... 
doi:10.1093/bib/bbab070 pmid:33822883 fatcat:a4hj2fhybrc6zlsq6xyiu6snmy

Acceleration Of Nucleotide Semi-Global Alignment With Adaptive Banded Dynamic Programming [article]

Hajime Suzuki, Masahiro Kasahara
2017 bioRxiv   pre-print
Our goal is to design a faster extension algorithm suitable for single-molecule sequencers with high sequencing error rates (e.g., 10-15%) and with more frequent insertions and deletions than substitutions  ...  Pairwise alignment of nucleotide sequences has previously been carried out using the seed-and-extend strategy, where we enumerate seeds (shared patterns) between sequences and then extend the seeds by  ...  We also thank Professor Shinichi Morishita for his kind and insightful comment on this manuscript.  ... 
doi:10.1101/130633 fatcat:ostn3u6oejclbanwznilspczde

Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design [article]

Mohammed H K Alser
2019 arXiv   pre-print
in the reference genome do not align with a given read due to high dissimilarity.  ...  The first key idea of our pre-alignment filters is to provide high filtering accuracy by correctly detecting all similar segments shared between two sequences.  ...  Pairwise alignment is a way to identify regions of high similarity between sequences.  ... 
arXiv:1910.03936v1 fatcat:f2sw22g2sndc5b3jasnaoizw7i

A Customized Many-Core Hardware Acceleration Platform for Short Read Mapping Problems Using Distributed Memory Interface with 3D–Stacked Architecture

Pei Liu, Ahmed Hemani, Kolin Paul, Christian Weis, Matthias Jung, Norbert Wehn
2016 Journal of Signal Processing Systems  
The processing core is highly customized to suite both 2-hit string matching and banded Smith-Waterman sequence alignment operations, while distributed memory interface with 3Dstacked architecture provides  ...  high bandwidth and low access latency for highly customized dataset partitioning and memory access scheduling.  ...  Acknowledgements We are very grateful to Professor Lars Arvestad for providing many valuable suggestions.  ... 
doi:10.1007/s11265-016-1204-8 fatcat:fmfr633cdjc3tmfkoksgwmk6za
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