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A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences

Aleksandr Morgulis, E. Michael Gertz, Alejandro A. Schäffer, Richa Agarwala
2006 Journal of Computational Biology  
The DUST module has been used within BLAST for many years to mask low-complexity sequences.  ...  In this paper, we present a new implementation of the DUST module that uses the same function to assign a complexity score to a sequence, but uses a different rule by which high-scoring sequences are masked  ...  One would like masking of low-complexity sequences to be as fast and as predictable as possible.  ... 
doi:10.1089/cmb.2006.13.1028 pmid:16796549 fatcat:m6fjszvoazambev3qon3u3ns2u

Cookiecutter: a tool for kmer-based read filtering and extraction [article]

Ekaterina Starostina, Gaik Tamazian, Pavel Dobrynin, Stephen O'Brien, Aleksey Komissarov
2015 bioRxiv   pre-print
Cookiecutter is based on the implementation of the Aho-Corasik algorithm and is useful in routine processing of high-throughput sequencing datasets.  ...  A number of read processing routines include extracting or removing sequence reads from the results of highthroughput sequencing experiments prior to further analysis.  ...  Low complexity detection The symmetric DUST algorithm (Morgulis et al., 2006) was designed to mask lowcomplexity sequence reads.  ... 
doi:10.1101/024679 fatcat:w43kz2vzcjhmnk6cxxvcc3izxy

populacDNA normalization by hydroxyapatite chromatography to enrich transcriptome diversity in RNA-seq applications

Victoria A. VanderNoot, Stanley A. Langevin, Owen D. Solberg, Pamela D. Lane, Deanna J. Curtis, Zachary W. Bent, Kelly P. Williams, Kamlesh D. Patel, Joseph S. Schoeniger, Steven S. Branda, Todd W. Lane
2012 BioTechniques  
Low-quality tails were trimmed from reads in the manner of bwa (1), library primer sequences were then trimmed from reads, and low-complexity sequence was masked with DUST (2).  ...  Low-complexity sequence was then unmasked for the retained reads.  ...  Bioinformatics 25:1754-1760. 2.Morgulis, A., Gertz, E.M., Schaffer, A.A., and Agarwala, R. 2006. A fast and symmetric DUST implementation to mask low-com- plexity DNA sequences.  ... 
doi:10.2144/000113937 pmid:23227988 fatcat:pucpvccldnc4xj6m3b7zrfjejm

New synthetic-diploid benchmark for accurate variant calling evaluation [article]

Heng Li, Jonathan M Bloom, Yossi Farjoun, Mark Fleharty, Laura D Gauthier, Benjamin Neale, Daniel MacArthur
2017 bioRxiv   pre-print
This benchmark provides a more accurate and less biased estimate of the error rate of small variant calls in a realistic context.  ...  We derived a new benchmark dataset from the de novo PacBio assemblies of two human cell lines that are homozygous across the whole genome.  ...  A. & Agarwala, R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 13, 1028-1040, doi:10.1089/cmb.2006.13.1028 (2006). 23 Mallick, S. et al.  ... 
doi:10.1101/223297 fatcat:gc2bgedjrranxisp4jhld3wym4

Advanced photonic and electronic systems WILGA 2016

Ryszard S. Romaniuk
2016 International Journal of Electronics and Telecommunications  
Wilga, gathering through years the organization experience, has turned out to be a perfect relevant information exchange platform between young researchers from Poland with participation of international  ...  Young Researchers Symposium WILGA on Photonics Applications and Web Engineering has been organized since 1998, two times a year.  ...  The algorithm is efficient, fast, low latency and allows GEM detector switching to the online mode.  ... 
doi:10.1515/eletel-2016-0042 fatcat:r6s5ba2yxfc7lmi5dede3wfvli

Probing the diversity of healthy oral microbiome with bioinformatics approaches

Ji-Hoi Moon, Jae-Hyung Lee
2016 BMB Reports  
With rapid advances in DNA sequencing and analytical technologies, population-based studies have documented the range and diversity of both taxonomic compositions and functional potentials observed in  ...  The human oral cavity contains a highly personalized microbiome essential to maintaining health, but capable of causing oral and systemic diseases.  ...  Morgulis A, Gertz EM, Schäffer AA and Agarwala R (2006) A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 13, 1028-1040 25.  ... 
doi:10.5483/bmbrep.2016.49.12.164 pmid:27697111 pmcid:PMC5346311 fatcat:mx3wrwj3orgg3m5qqtzd2q2z2y

Making sense of score statistics for sequence alignments

M. Pagni
2001 Briefings in Bioinformatics  
This paper aims to highlight a few of the principles that should be kept in mind when evaluating the statistical signi®cance of alignments between sequences.  ...  A few types of random sequence databases used in the estimation of statistical signi®cance are presented, and the statistics employed by the BLAST, FASTA and PRSS programs are compared.  ...  Acknowledgements We wish to thank Philipp Bucher, Ste Âphane Vuilleumier and Thomas Junier for their helpful comments during the preparation of this manuscript.  ... 
doi:10.1093/bib/2.1.51 pmid:11465063 fatcat:m53iocquwjfgrdsjhindhutckq

Contrasting signatures of genomic divergence during sympatric speciation

Andreas F. Kautt, Claudius F. Kratochwil, Alexander Nater, Gonzalo Machado-Schiaffino, Melisa Olave, Frederico Henning, Julián Torres-Dowdall, Andreas Härer, C. Darrin Hulsey, Paolo Franchini, Martin Pippel, Eugene W. Myers (+1 others)
2020 Nature  
By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence.  ...  Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species.  ...  This modified version stitches short alignment artefacts resulting from bad sequencing segments within overlapping read pairs to align through low complexity or tandem repeat elements without creating  ... 
doi:10.1038/s41586-020-2845-0 pmid:33116308 fatcat:gbyzz47t4faf5mq3mu2qnqtit4

Photonics and Web Engineering 2011

Ryszard Romaniuk
2011 International Journal of Electronics and Telecommunications  
It is also an occasion for young researchers to meet together in a large group (under the patronage of IEEE) spanning the whole country with guests from this part of Europe.  ...  A digest of Wilga references is presented [1-92].  ...  For a particular complex sound, there is created a specific masking curve.  ... 
doi:10.2478/v10177-011-0058-z fatcat:ns3panw3prawje2iauj2l3dkhq

Humans are colonized by many uncharacterized and highly divergent microbes [article]

Mark Alec Kowarsky, Joan Camunas-Soler, Michael Kertesz, Iwijn De Vlaminck, Lian Chye Winston Koh, Wenying Pan, Lance Martin, Norma Neff, Jennifer Okamoto, Ronald J Wong, Sandhya Kharbanda, Yasser El-Sayed (+5 others)
2017 bioRxiv   pre-print
Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome  ...  Analysing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little  ...  Correspondence and requests for materials should be addressed to quake@stanford.edu  ... 
doi:10.1101/113746 fatcat:7bq4pspznfb6hlsemezoz6riza

HELLO: A hybrid variant calling approach [article]

Anand Ramachandran, Steven S. Lumetta, Eric Klee, Deming Chen
2020 bioRxiv   pre-print
We also find improvements in calling small indels in low-complexity regions.  ...  However, these reads have context-dependent indel errors in low-complexity regions, resulting in lower accuracy of small indel calls compared to NGS reads.  ...  CNS 1624790, and CNS 1337732.  ... 
doi:10.1101/2020.03.23.004473 fatcat:4r4ol7z67famjnuwztdizj5mg4

Physical Principles and Visual-OMP Software for Optimal PCR Design [chapter]

John SantaLucia
2007 Msphere  
In multiplex and other complex assays, however, the design flaws from matched T m 's become crucial and lead to failure.  ...  BLAST also uses a minimum 8 nt "word length," which must be a perfect match; this is used to make the BLAST algorithm fast, but it also means that BLAST will miss structures that have fewer than eight  ...  Acknowledgments I am thankful to all my previous graduate students and coworkers at DNA Software, Inc. for their hard work and contributions to the fields of DNA thermodynamics and software development  ... 
doi:10.1007/978-1-59745-528-2_1 pmid:17951788 fatcat:tghqvlsslzcspmi673q4m4q32m

Microarray Technology and Applications in Environmental Microbiology [chapter]

Jizhong Zhou, Dorothea K Thompson
2004 Advances in Agronomy  
While oligonucleotide microarrays are limited to array elements of low sequence complexity, the specificity of hybridization for a complex probe is improved with arrays containing DNA fragments that are  ...  The advantages of microspotting include ease of implementation, low cost, and versatility, while a major disadvantage is that each sample to be arrayed must be prepared, purified, and stored prior to microarray  ... 
doi:10.1016/s0065-2113(03)82004-7 fatcat:mrkm4hlo2nbbfev6efao6j3vb4

A Draft Human Pangenome Reference [article]

Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian K. Lucas, Jean Monlong, Haley J. Abel, Silvia Buonaiuto, Xian H. Chang (+45 others)
2022 bioRxiv   pre-print
euchromatic polymorphic sequence and 1,529 gene duplications relative to the existing reference, GRCh38.  ...  Based on alignments of the assemblies, we generated a draft pangenome that captures known variants and haplotypes, reveals novel alleles at structurally complex loci, and adds 119 million base pairs of  ...  Acknowledgements We would like to acknowledge Shelby Bidwell and other members of the GenBank staff at the National Center for Biotechnology Information (NCBI; NLM/NIH) for their work to release the assemblies  ... 
doi:10.1101/2022.07.09.499321 fatcat:bvxwif7awzbk7ikcdt7xk2g4xy

Recent progress in SERS biosensing

Kyle C. Bantz, Audrey F. Meyer, Nathan J. Wittenberg, Hyungsoon Im, Özge Kurtuluş, Si Hoon Lee, Nathan C. Lindquist, Sang-Hyun Oh, Christy L. Haynes
2011 Physical Chemistry, Chemical Physics - PCCP  
While the formation of DNA-NP complexes is generally used for the detection of specific binding events, the complex formed between DNA, or DNA-like molecules, and NPs can also be used to create SERS hotspots  ...  Graham and coworkers found that DNA hybridization was observed only when a fully complementary DNA sequence was added to their DNA-functionalized Ag NPs, 87 proving that they could detect single nucleotide  ... 
doi:10.1039/c0cp01841d pmid:21509385 pmcid:PMC3156086 fatcat:laemfgc2prg5dkggxbn225atae
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