scholarly journals NASCUP: Nucleic Acid Sequence Classification by Universal Probability

IEEE Access ◽  
2021 ◽  
pp. 1-1
Author(s):  
Sunyoung Kwon ◽  
Gyuwan Kim ◽  
Byunghan Lee ◽  
Jongsik Chun ◽  
Sungroh Yoon ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Sequence ◽  
Sequence Classification

scholarly journals CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8965
Author(s):  
He Peng
Keyword(s):  
Experimental Data ◽  
Feature Extraction ◽  
Nucleic Acid ◽  
Large Scale ◽  
Extraction Methods ◽  
Nucleic Acid Sequence ◽  
Sequence Classification ◽  
Long Distance ◽  
Frequent Sequence ◽  
Nucleic Acid Sequences

Background Conserved nucleic acid sequences play an essential role in transcriptional regulation. The motifs/templates derived from nucleic acid sequence datasets are usually used as biomarkers to predict biochemical properties such as protein binding sites or to identify specific non-coding RNAs. In many cases, template-based nucleic acid sequence classification performs better than some feature extraction methods, such as N-gram and k-spaced pairs classification. The availability of large-scale experimental data provides an unprecedented opportunity to improve motif extraction methods. The process for pattern extraction from large-scale data is crucial for the creation of predictive models. Methods In this article, a Teiresias-like feature extraction algorithm to discover frequent sub-sequences (CFSP) is proposed. Although gaps are allowed in some motif discovery algorithms, the distance and number of gaps are limited. The proposed algorithm can find frequent sequence pairs with a larger gap. The combinations of frequent sub-sequences in given protracted sequences capture the long-distance correlation, which implies a specific molecular biological property. Hence, the proposed algorithm intends to discover the combinations. A set of frequent sub-sequences derived from nucleic acid sequences with order is used as a base frequent sub-sequence array. The mutation information is attached to each sub-sequence array to implement fuzzy matching. Thus, a mutate records a single nucleotide variant or nucleotides insertion/deletion (indel) to encode a slight difference between frequent sequences and a matched subsequence of a sequence under investigation. Conclusions The proposed algorithm has been validated with several nucleic acid sequence prediction case studies. These data demonstrate better results than the recently available feature descriptors based methods based on experimental data sets such as miRNA, piRNA, and Sigma 54 promoters. CFSP is implemented in C++ and shell script; the source code and related data are available at https://github.com/HePeng2016/CFSP.

Gold-Aptamer-Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences

2019 ◽  
Author(s):  
Veeren Chauhan ◽  
Mohamed M Elsutohy ◽  
C Patrick McClure ◽  
Will Irving ◽  
Neil Roddis ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
In Silico ◽  
Point Of Care ◽  
Lateral Flow ◽  
Nucleic Acid Sequence ◽  
In Silico Screening ◽  
Lateral Flow Assays ◽  
Life Threatening ◽  
Software And Hardware ◽  
Nucleic Acid Sequences

<p>Enteroviruses are a ubiquitous mammalian pathogen that can produce mild to life-threatening disease. Bearing this in mind, we have developed a rapid, accurate and economical point-of-care biosensor that can detect a nucleic acid sequences conserved amongst 96% of all known enteroviruses. The biosensor harnesses the physicochemical properties of gold nanoparticles and aptamers to provide colourimetric, spectroscopic and lateral flow-based identification of an exclusive enteroviral RNA sequence (23 bases), which was identified through in silico screening. Aptamers were designed to demonstrate specific complementarity towards the target enteroviral RNA to produce aggregated gold-aptamer nanoconstructs. Conserved target enteroviral nucleic acid sequence (≥ 1x10<sup>-7</sup> M, ≥1.4×10<sup>-14</sup> g/mL), initiates gold-aptamer-nanoconstructs disaggregation and a signal transduction mechanism, producing a colourimetric and spectroscopic blueshift (544 nm (purple) > 524 nm (red)). Furthermore, lateral-flow-assays that utilise gold-aptamer-nanoconstructs were unaffected by contaminating human genomic DNA, demonstrated rapid detection of conserved target enteroviral nucleic acid sequence (< 60 s) and could be interpreted with a bespoke software and hardware electronic interface. We anticipate our methodology will translate in-silico screening of nucleic acid databases to a tangible enteroviral desktop detector, which could be readily translated to related organisms. This will pave-the-way forward in the clinical evaluation of disease and complement existing strategies at overcoming antimicrobial resistance.</p>

Rapid and simultaneous detection of three major diarrhea-causing viruses by multiplex real-time nucleic acid sequence-based amplification

2015 ◽  
Vol 160 (3) ◽  
pp. 719-725 ◽  
Author(s):  
Qiu-Hua Mo ◽  
Hai-Bo Wang ◽  
Hui-Rong Dai ◽  
Ji-Can Lin ◽  
Hua Tan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Simultaneous Detection ◽  
Nucleic Acid Sequence

Complete nisin A gene cluster from Lactococcus lactis M78 (HM219853) — obtaining the nucleic acid sequence and comparing it to other published nisin sequences

2011 ◽  
Vol 33 (3) ◽  
pp. 217-221 ◽  
Author(s):  
Aljoša Trmčić ◽  
John Samelis ◽  
Christophe Monnet ◽  
Irena Rogelj ◽  
Bojana Bogovič Matijašić
Keyword(s):  
Nucleic Acid ◽  
Gene Cluster ◽  
Lactococcus Lactis ◽  
Nucleic Acid Sequence

Viral nucleic acid sequence transfer between fungi and plants

1997 ◽  
Vol 13 (7) ◽  
pp. 260-261 ◽  
Author(s):  
Joachim R. Marienfeld ◽  
Michael Unseld ◽  
Petra Brandt ◽  
Axel Brennicke
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Sequence ◽  
Viral Nucleic Acid

Nucleic Acid Sequence Database IV

DNA ◽  
1982 ◽  
Vol 1 (4) ◽  
pp. 365-374 ◽  
Author(s):  
H.R. CHEN ◽  
M.O. DAYHOFF ◽  
W.C. BARKER ◽  
L.T. HUNT ◽  
L.-S. YEH ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Sequence ◽  
Sequence Database

Nucleic acid sequence-based amplification (NASBA) detection of medically important Candida species

1999 ◽  
Vol 38 (1-2) ◽  
pp. 81-90 ◽  
Author(s):  
Myra N. Widjojoatmodjo ◽  
Annemarie Borst ◽  
Rianne A.F. Schukkink ◽  
Adrienne T.A. Box ◽  
Nicole M.M. Tacken ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Candida Species ◽  
Nucleic Acid Sequence

scholarly journals Real-Time Nucleic Acid Sequence-Based Amplification Assay for Detection of Hepatitis A Virus

2005 ◽  
Vol 71 (11) ◽  
pp. 7113-7116 ◽  
Author(s):  
Khaled H. Abd El Galil ◽  
M. A. El Sokkary ◽  
S. M. Kheira ◽  
Andre M. Salazar ◽  
Marylynn V. Yates ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Hepatitis A ◽  
Molecular Beacon ◽  
Hepatitis A Virus ◽  
Immunomagnetic Separation ◽  
Nucleic Acid Sequence ◽  
The Real ◽  
Nasba Assay ◽  
Environmental Pathogens

ABSTRACT A nucleic acid sequence-based amplification (NASBA) assay in combination with a molecular beacon was developed for the real-time detection and quantification of hepatitis A virus (HAV). A 202-bp, highly conserved 5′ noncoding region of HAV was targeted. The sensitivity of the real-time NASBA assay was tested with 10-fold dilutions of viral RNA, and a detection limit of 1 PFU was obtained. The specificity of the assay was demonstrated by testing with other environmental pathogens and indicator microorganisms, with only HAV positively identified. When combined with immunomagnetic separation, the NASBA assay successfully detected as few as 10 PFU from seeded lake water samples. Due to its isothermal nature, its speed, and its similar sensitivity compared to the real-time RT-PCR assay, this newly reported real-time NASBA method will have broad applications for the rapid detection of HAV in contaminated food or water.

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