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Examining coding structure and redundancy in DNA

G. Rosen
2006 IEEE Engineering in Medicine and Biology Magazine  
It is well known that these protein-coding regions have the lowest mutation rates in the DNA strand. So, the question arises: how does DNA protect itself from error?  ...  In this article, we develop a method to uncover an errorcorrection coding structure in the nucleotide sequence, and show that our framework is efficient for detecting approximate tandem repeats, such as  ...  Moore, now at Khimetrics, Inc., for invaluable discussions and his contribution to subspace partitioning method.  ... 
doi:10.1109/memb.2006.1578665 pmid:16485393 fatcat:3quid7fmnrfepbb7ojvqmvpe3u

SPIDER-WEB enables stable, repairable, and encryptible algorithms under arbitrary local biochemical constraints in DNA-based storage [article]

Haoling Zhang, Zhaojun Lan, Wenwei Zhang, Xun Xu, Zhi Ping, Yiwei Zhang, Yue Shen
2022 arXiv   pre-print
Despite the biochemical progress in DNA synthesis and sequencing, novel coding algorithms need to be constructed under the specific constraints in DNA-based storage.  ...  These generated coding algorithms could be used to encode arbitrary digital data as DNA sequences directly or served as a benchmark for the follow-up construction of coding algorithms.  ...  These well-established error-correcting codes provide an effective way to solve one or more substitution errors in DNA molecules.  ... 
arXiv:2204.02855v2 fatcat:buae2g7ojfacbi7uebwjcayeki

De novo sequencing and variant calling with nanopores using PoreSeq

Tamas Szalay, Jene A Golovchenko
2015 Nature Biotechnology  
algorithm for the error correction of nanopore data, utilizing 3 statistical models of the physical system in order to obtain high accuracy de novo sequences 4 at a range of coverage depths.  ...  In particular, the inclusion of current level durations will be 29 necessary in dealing with homopolymer DNA regions, which we have found are responsible for 30 8 over half of the errors at 99% accuracy  ...  We also used the algorithm to error-correct and assemble a previously published E. coli MinION 7 dataset 7 using a similar procedure to that for -DNA.  ... 
doi:10.1038/nbt.3360 pmid:26352647 pmcid:PMC4877053 fatcat:xip7mre4lnf7dd2at3ksxfw42i

Efficient Exonic Regions Prediction in DNA Sequence Using Fast Converged Adaptive Filter

Y. Murali Krishna, K. Murali Krishna, Ch. Amaranatha Sarma
2013 International Journal of Signal Processing, Image Processing and Pattern Recognition  
Secondly the filtering scheme for genomic signal processing with periodic behavior in biological sequence is introduced, which can predict and analyze the biological region that are interested in. finally  ...  First using the electron ion potential method the symbolic DNA sequences are converted in to digital signal.  ...  To improve the traditional Fourier analysis performance in distinguishing coding from non-coding regions in a DNA sequence an optimization procedure has been used.  ... 
doi:10.14257/ijsip.2016.9.5.21 fatcat:rblssgxlnbgslgb3axhl7mfffe

DNA Barcoding through Quaternary LDPC Codes

Elizabeth Tapia, Flavio Spetale, Flavia Krsticevic, Laura Angelone, Pilar Bulacio, Lars Kaderali
2015 PLoS ONE  
To address these competitive requirements, the use of error-correcting codes is advised.  ...  For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded.  ...  Acknowledgments ET's, FS's, FK's, LA's and PB's work was supported by project PICT 2012-2513, "Multiplex systems for targeted microfluidic amplification and NGS sequencing", National Agency for Science  ... 
doi:10.1371/journal.pone.0140459 pmid:26492348 pmcid:PMC4619643 fatcat:ndtpjacccjhnlnsd6m5br7ypr4

Finding Data in DNA: Computer Forensic Investigations of Living Organisms [chapter]

Marc B. Beck, Eric C. Rouchka, Roman V. Yampolskiy
2013 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
Several methods have been developed to insert information into a DNA sequence for the purpose of data storage, watermarking, or communication of secret messages.  ...  Recent advances in genetic engineering have allowed the insertion of artificial DNA strands into the living cells of organisms.  ...  form of error detection and error correction since a mutation can destroy the encrypted message in the DNA sequence.  ... 
doi:10.1007/978-3-642-39891-9_13 fatcat:6dt67raytrcnlgne3l7lwlfqyq

Discovery of Highly Accurate Plant DNA Barcodes via Novel Iterative Methodologies

Jaison Jain
2015 International Journal of Biology  
Moreover, an algorithm was constructed to optimize this novel process, yielding a 17000% increase in efficiency.  ...  chloroplast sequences.  ...  Acknowledgements I would like to acknowledge Julian Glowacz for his guidance on algorithm design and Ms. Gilana Reiss for her general research consultations and guidance.  ... 
doi:10.5539/ijb.v7n4p42 fatcat:akjo4b34indzrfieh7disbna4y

An error-correcting code framework for genetic sequence analysis

Elebeoba E. May, Mladen A. Vouk, Donald L. Bitzer, David I. Rosnick
2004 Journal of the Franklin Institute  
Extending beyond specific genomic regions and sequences, MacDonaill [26] develops an EC coding model for nucleic acid sequences in general.  ...  Reif and LaBean [46] propose EC coding-based methods for the development of errorcorrection strands for repairing errors in DNA chips.  ...  This work was supported in part by a National Science Foundation Minority Graduate Fellowship and the Ford Foundation Dissertation Fellowship for Minorities.  ... 
doi:10.1016/j.jfranklin.2003.12.009 fatcat:6ohtuce7snhpfijcj5uuzflo54

Indel-correcting DNA barcodes for high-throughput sequencing

John A. Hawkins, Stephen K. Jones, Ilya J. Finkelstein, William H. Press
2018 Proceedings of the National Academy of Sciences of the United States of America  
Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions  ...  Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations.  ...  We thank James Rybarski, Andrea Hawkins-Daarud, Jeffrey Hussmann, Prakash Mohan, Alexander Boulgakov, and Kevin Drew for useful feedback throughout the project.  ... 
doi:10.1073/pnas.1802640115 pmid:29925596 fatcat:sjc2vkafxndkvhelo7wgux7jkm

Using a VOM model for reconstructing potential coding regions in EST sequences

Armin Shmilovici, Irad Ben-Gal
2007 Computational statistics (Zeitschrift)  
This paper presents a method for annotating coding and noncoding DNA regions by using variable order Markov (VOM) models.  ...  The paper presents a modified VOM model for detecting and correcting insertion and deletion sequencing errors that are commonly found in ESTs.  ...  Yet, here, unlike in the previous section, the correct phase of the coding regions in unknown. Discussion Recognition of coding DNA regions is an important phase of any gene-finder procedure.  ... 
doi:10.1007/s00180-007-0021-8 fatcat:wova757tmfgjhkldhfqnuqq6si

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

A. Loytynoja, N. Goldman
2008 Science  
Sequence Alignment and Evolutionary Analysis Phylogeny-Aware Gap Placement Prevents Errors in www.sciencemag.org (this information is current as of September 4, 2008 ): The following resources related  ...  region evolves through short insertions and deletions, allowing for rapid and radical changes in the coding sequence (Fig. 1B) .  ...  Naïve iteration of pairwise alignment penalizes this single evolutionary event multiple times (orange triangles), giving an inappropriately high cost for the correct alignment.  ... 
doi:10.1126/science.1158395 pmid:18566285 fatcat:xfdarg5f6zcrpoxyjyxa2yf42a

DIANA-EST: a statistical analysis

A. G. Hatzigeorgiou, P. Fiziev, M. Reczko
2001 Bioinformatics  
The correct prediction of the end of the coding region was predicted in 43 cases correct from ESTscan and for 56 sequences correct from DIANA-EST.  ...  If the sequence is derived from a coding region without sequencing errors the output will be a number series with a high score in every third position.  ...  comments, to Amos Bairoch for providing the dataset and to the anonymous reviewers for helpful comments.  ... 
doi:10.1093/bioinformatics/17.10.913 pmid:11673235 fatcat:g326spouuvghzjgu4fgk2tmghy

Message from the general chairs

Ramesh Jain, Mohan Kumar
2008 2008 International Symposium on a World of Wireless, Mobile and Multimedia Networks  
Such synchronization errors are likely to occur during DNA sequencing and may lead to serve problems in decoding the DNA barcodes.  ...  DNA sequences, which were introduced by Head in 1987.  ... 
doi:10.1109/wowmom.2008.4594797 dblp:conf/wowmom/JainK08 fatcat:ziu25issdvga7cmqjgbtqtdu7q

Optimized Code Design for Constrained DNA Data Storage with Asymmetric Errors

Li Deng, Yixin Wang, Md. Noor-A-Rahim, Yong Liang Guan, Zhiping Shi, Erry Gunawan, Chueh Loo Poh
2019 IEEE Access  
occurrence and correct asymmetric substitution errors.  ...  Her research interests include coding for deoxyribonucleic acid data storage, constrained codes, and error control codes.  ...  For the Illumina sequencer channel in Fig. 10 , the BER curves of the compared rate 5/6 codes decrease slowly in the practical error region, where the sharp waterfall regions could not be observed.  ... 
doi:10.1109/access.2019.2924827 fatcat:gk7o4nkyprg4bhjeaaychsadfi

CLGBO: An Algorithm for Constructing Highly Robust Coding Sets for DNA Storage

Yanfen Zheng, Jieqiong Wu, Bin Wang
2021 Frontiers in Genetics  
This helps to resolve the problem that arises when consecutive repetitive subsequences in the sequence cause errors in DNA storage.  ...  In this study, we describe an enhanced gradient-based optimizer that includes the Cauchy and Levy mutation strategy (CLGBO) to construct DNA coding sets, which are used as primer and address libraries.  ...  At present, Reed-Solomon codes (RS codes) are the main error-correction method. In 2015, Grass et al. (2015) applied RS coding to DNA storage for error-free storage.  ... 
doi:10.3389/fgene.2021.644945 pmid:34017354 pmcid:PMC8129200 fatcat:jsvvz6uxfrfmzjk2uwhsuhwb2a
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