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Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences

Tatsuhiko TSUNODA, Masao FUKAGAWA, Toshihisa TAKAGI
1998 Biocomputing '99  
Genomic science and structural biology meet in the relationship between the sequence and the structure of nucleic acids.  ...  Particularly, the same sequence which appears in a dierent place such as a palindromic or repetitive sequence has biophysical meaning: recognition site of dimers, forming stem-loops, and contributions  ...  Acknowledgements This work is partially supported by Grant-in-Aid for Scientic Research on Priority Areas, \Genome Science" from the Ministry of Education, Science, Sports, and Culture, Japan.  ... 
doi:10.1142/9789814447300_0020 fatcat:74wsnnzbhrdm3e2b5abf745yqa

A Novel Frequency Based Feature Extraction Technique for Classification of Corona Virus Genome and Discovery of COVID-19 Repeat Pattern

Muthulakshmi Murugaiah, Murugeswari Ganesan
2021 Brazilian Archives of Biology and Technology  
In this article, we propose a novel feature extraction technique called Frequency based Feature Extraction Technique which extracts 120 features from genome sequences for classification.  ...  Feature Extraction plays a crucial role in classification as it is used to convert the Genome sequences into a set of quantitative values.  ...  Liu Z and coauthors [9] developed a feature extraction algorithm for Genome sequences.  ... 
doi:10.1590/1678-4324-2021210075 fatcat:2t22r36vxfes7dpepdrpi7ztdy

Lossless Compression Algorithms [chapter]

Ze-Nian Li, Mark S. Drew, Jiangchuan Liu
2014 Texts in Computer Science  
In this paper, we comparatively survey the main ideas and results of lossless compression algorithms that have been developed for DNA sequences.  ...  Recently, new algorithms have been introduced specifically for this purpose.  ...  Searching for approximate repeats takes a long time and requires a large amount of memory.  ... 
doi:10.1007/978-3-319-05290-8_7 fatcat:vyv2p3xwcvbe3oz32bnmjuvray

High-throughput DNA sequence data compression

Z. Zhu, Y. Zhang, Z. Ji, S. He, X. Yang
2013 Briefings in Bioinformatics  
In this article, we categorize and provide a comprehensive review of the existing compression methods specialized for genomic data and present experimental results on compression ratio, memory usage, time  ...  for compression and decompression.  ...  The performances of different algorithms differ mainly based on how many repetitive subsequences can be identified and how efficiently they can be encoded.  ... 
doi:10.1093/bib/bbt087 pmid:24300111 fatcat:kneiduikjrak5k2em4enzcsnfa

Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genorne

Byung-Jun Yoon, P.P. Vaidyanathan
2007 IEEE Signal Processing Magazine  
The RNA is a nucleic acid that consists of a string of nucleotides (or bases), A, C, G and U, where uracil (U) is chemically similar to thymine (T) in the DNA.  ...  However, to use profile-csHMMs in practical applications, we need an efficient algorithm for finding the best alignment between the model and an observation sequence in a systematic way.  ... 
doi:10.1109/msp.2007.273058 fatcat:er6ktap6bnaxvmhe4l56etc7l4

A rapid method for detection of putative RNAi target genes in genomic data

Y. Horesh, A. Amir, S. Michaeli, R. Unger
2003 Bioinformatics  
The other method looks for synteny between C.elegans and C.briggsae assuming that genes that might be under RNAi control in both organisms are more likely to be biological significant.  ...  The method is based on scanning the genomes using a suffix tree data structure that was specifically modified to identify sets of combinations of repeated and inverted repeated sequences of 20 bp or more  ...  ACKNOWLEDGMENTS Ron Unger and Amihood Amir are partially supported by the Bikura foundation of the Israeli Academy of Science.  ... 
doi:10.1093/bioinformatics/btg1063 pmid:14534175 fatcat:rpddmoghsnbapb2cpjvud7veva

An efficient algorithm for identifying matches with errors in multiple long molecular sequences

Ming-Ying Leung, B. Edwin Blaisdell, Chris Burge, Samuel Karlin
1991 Journal of Molecular Biology  
An efficient algorithm is described for finding matches, repeats and other word relations, allowing for errors, in large data sets of long molecular sequences.  ...  The average memory and run time requirement both increase almost linearly with the total sequence length.  ...  ., C.B. and S.K. are supported in part by NIH Grants HG00335-03 and GM10452-28 and NSF grant DMS86-06244.  ... 
doi:10.1016/0022-2836(91)90938-3 pmid:1942056 pmcid:PMC4076298 fatcat:36l5rivdajcyjdd6cpp7aduvea

To Detect and Analyze Sequence Repeats Whatever Be Their Origin [chapter]

Jacques Nicolas
2012 Msphere  
Second, the huge increase of sequence production capacities requires to use the most efficient data structures and algorithms to scale up tools in front of the data deluge.  ...  Running title: To detect and to analyze sequence repeats 1 1 31 i.  ...  Acknowledgement This work was supported in part by a grant from the Agence Nationale de la Recherche [project Modulome ANR-05-MMSA-0010-01].  ... 
doi:10.1007/978-1-61779-603-6_4 pmid:22367866 fatcat:pb7f6hex3bgzfepa33ojoas4ui

Uncertainties in synthetic DNA-based data storage

Chengtao Xu, Chao Zhao, Biao Ma, Hong Liu
2021 Nucleic Acids Research  
Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption  ...  Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties  ...  After the encoding step, the DNA sequences are obtained for the next synthesis step. Writing Current nucleic acid synthesis methods are based on chemical or enzymatic methods.  ... 
doi:10.1093/nar/gkab230 pmid:33836076 fatcat:vy2anebyynb4llbqrchlynd46i

Finding and Characterizing Repeats in Plant Genomes [chapter]

Jacques Nicolas, Pierre Peterlongo, Sébastien Tempel
2016 Msphere  
The second section introduces the key concepts that are useful for understanding the current state of the art in playing with words, applied to genomic sequences.  ...  The last section introduces concepts and practical tools that can be used to reach this syntactic level in biological sequence analysis.  ...  of the analyzed string (nucleic acids A, C or T in our example).  ... 
doi:10.1007/978-1-4939-3167-5_17 pmid:26519414 fatcat:j47bdlqwibhxzifuzkfccppuve

A novel cause of chronic viral meningoencephalitis: Cache Valley virus

Michael R. Wilson, Dan Suan, Andrew Duggins, Ryan D. Schubert, Lillian M. Khan, Hannah A. Sample, Kelsey C. Zorn, Aline Rodrigues Hoffman, Anna Blick, Meena Shingde, Joseph L. DeRisi
2017 Annals of Neurology  
Acknowledgment Research reported in this article was supported by the UCSF Center for Next-Gen Precision Diagnostics supported by the Sandler Foundation and William K.  ...  A common issue in metagenomic sequencing is that essentially all reagents used during the library preparation process contain some extraneous nucleic acid, including material commonly present in laboratory  ...  Global surveillance efforts need to be streamlined, because it is both time-consuming and costly for physicians to order many pathogen-specific tests for geographically and clinically novel organisms.  ... 
doi:10.1002/ana.24982 pmid:28628941 pmcid:PMC5546801 fatcat:enf7aroprrdelhbyljhflb7srm

Harnessing CRISPR-Cas to Combat COVID-19: From Diagnostics to Therapeutics

Kok Gan Chan, Geik Yong Ang, Choo Yee Yu, Chan Yean Yean
2021 Life  
Viral nucleic acid detection via real-time reverse transcription polymerase chain reaction (rRT-PCR) or sequencing is regarded as the gold standard for COVID-19 diagnosis, but these technically intricate  ...  In this review, we highlight the recent advances in CRISPR–Cas-based nucleic acid detection strategies and the application of CRISPR–Cas as a potential antiviral agent in the context of COVID-19.  ...  The CRISPR array is transcribed and further processed into crRNA (2) and upon subsequent attack by the same invader, the spacer will guide the Cas protein to cleave the invading nucleic acid sequence (  ... 
doi:10.3390/life11111210 pmid:34833086 pmcid:PMC8623262 fatcat:t3grs467s5ahflwfshiir6mgpy

DNA N6-Methyladenine Modification in Plant Genomes—A Glimpse into Emerging Epigenetic Code

Jeyalakshmi Karanthamalai, Aparna Chodon, Shailja Chauhan, Gopal Pandi
2020 Plants  
The current review article emphasizes the research advances in DNA 6mA modifications, identification, available databases, analysis tools and its significance in plant development, cellular functions and  ...  Though 6mA information is less known, the available evidences suggest its function in plant development, tissue differentiation, and regulations in gene expression.  ...  Among the various epigenetic alteration in nucleic acids and histones, DNA methylation plays pivotal roles to establish control in gene expression, pairing between the bases, positioning and stability  ... 
doi:10.3390/plants9020247 pmid:32075056 pmcid:PMC7076483 fatcat:hiyz7w3rbvdrjebev44xvg247i

Artificial intelligence and molecular biology

1994 ChoiceReviews  
See [Baddeley, 1986] for an overview of algorithms for two-dimensional segmentation.  ...  The depict slot is not illustrated in the frame in Figure 2 since this function is constant for all images.  ...  The algorithm recursively recomputes the same answer -the T value -for each subsequence many times.  ... 
doi:10.5860/choice.31-3826 fatcat:5jmryy7mkbcrvifz6ahlbbdceu

PRAP: an ab initio software package for automated genome-wide analysis of DNA repeats for prokaryotes

Gwo-Liang Chen, Yun-Juan Chang, Chun-Hway Hsueh
2013 Bioinformatics  
Deciphering all repeats in DNA sequences is an important and open task in genome annotation and bioinformatics.  ...  It is currently the most complete repeat finder for prokaryotes and is a valuable tool for genome annotation.  ...  The authors thank National Science Council (NSC), Taiwan, for the supporting grant, and the facilities in National Taiwan University and HPCbio, the University of Illinois to complete this work.  ... 
doi:10.1093/bioinformatics/btt482 pmid:23958725 fatcat:eq7eeejsifgpbh25s25so2ykq4
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