Next Generation DNA Sequencing Technologies and Applications

2010 ◽  
pp. 35-56
Author(s):  
Qingshu Meng ◽  
Jun Yu
Keyword(s):  
Dna Sequencing ◽  
Next Generation ◽  
Next Generation Dna Sequencing ◽  
Sequencing Technologies

scholarly journals Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1419 ◽  
Author(s):  
Jose E. Kroll ◽  
Jihoon Kim ◽  
Lucila Ohno-Machado ◽  
Sandro J. de Souza
Keyword(s):  
Alternative Splicing ◽  
Dna Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Software Suite ◽  
Next Generation Dna Sequencing ◽  
Sequencing Technologies ◽  
Body Map ◽  
Sequencing Platforms

Motivation.Alternative splicing events (ASEs) are prevalent in the transcriptome of eukaryotic species and are known to influence many biological phenomena. The identification and quantification of these events are crucial for a better understanding of biological processes. Next-generation DNA sequencing technologies have allowed deep characterization of transcriptomes and made it possible to address these issues. ASEs analysis, however, represents a challenging task especially when many different samples need to be compared. Some popular tools for the analysis of ASEs are known to report thousands of events without annotations and/or graphical representations. A new tool for the identification and visualization of ASEs is here described, which can be used by biologists without a solid bioinformatics background.Results.A software suite namedSplicing Expresswas created to perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms. Its major goal is to serve the needs of biomedical researchers who do not have bioinformatics skills.Splicing Expressperforms automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. The identification of ASEs is done by a known algorithm previously implemented in another tool namedSplooce. As a final result,Splicing Expresscreates a set of HTML files composed of graphics and tables designed to describe the expression profile of ASEs among all analyzed samples. By using RNA-Seq data from the Illumina Human Body Map and the Rat Body Map, we show thatSplicing Expressis able to perform all tasks in a straightforward way, identifying well-known specific events.Availability and Implementation.Splicing Expressis written in Perl and is suitable to run only in UNIX-like systems. More details can be found at:http://www.bioinformatics-brazil.org/splicingexpress.

Next-Generation DNA Sequencing Technologies

2014 ◽  
Vol 36 (3) ◽  
pp. 99-103 ◽  
Author(s):  
Gulsum Kayman Kurekci ◽  
Pervin Dincer
Keyword(s):  
Dna Sequencing ◽  
Next Generation ◽  
Next Generation Dna Sequencing ◽  
Sequencing Technologies

scholarly journals The near demise and subsequent revival of classical genetics for investigating Caenorhabditis elegans embryogenesis: RNAi meets next-generation DNA sequencing

2011 ◽  
Vol 22 (19) ◽  
pp. 3556-3558 ◽  
Author(s):  
Bruce Bowerman
Keyword(s):  
Caenorhabditis Elegans ◽  
Dna Sequencing ◽  
Reverse Genetics ◽  
Molecular Genetic ◽  
Biological Processes ◽  
Next Generation ◽  
Next Generation Dna Sequencing ◽  
C Elegans ◽  
Sequencing Technologies ◽  
Classical Genetics

Molecular genetic investigation of the early Caenorhabditis elegans embryo has contributed substantially to the discovery and general understanding of the genes, pathways, and mechanisms that regulate and execute developmental and cell biological processes. Initially, worm geneticists relied exclusively on a classical genetics approach, isolating mutants with interesting phenotypes after mutagenesis and then determining the identity of the affected genes. Subsequently, the discovery of RNA interference (RNAi) led to a much greater reliance on a reverse genetics approach: reducing the function of known genes with RNAi and then observing the phenotypic consequences. Now the advent of next-generation DNA sequencing technologies and the ensuing ease and affordability of whole-genome sequencing are reviving the use of classical genetics to investigate early C. elegans embryogenesis.

Next-generation DNA sequencing

2008 ◽  
Vol 26 (10) ◽  
pp. 1135-1145 ◽  
Author(s):  
Jay Shendure ◽  
Hanlee Ji
Keyword(s):  
Dna Sequencing ◽  
Next Generation ◽  
Next Generation Dna Sequencing

The mycobiome of the oral cavity in healthy dogs and dogs with periodontal disease

2022 ◽  
pp. 1-8
Author(s):  
Brook A. Niemiec ◽  
Jerzy Gawor ◽  
Shuiquan Tang ◽  
Aishani Prem ◽  
Janina A. Krumbeck
Keyword(s):  
Oral Cavity ◽  
Periodontal Disease ◽  
Dna Sequencing ◽  
Fungal Species ◽  
Next Generation ◽  
Data Set ◽  
Next Generation Dna Sequencing ◽  
Sequencing Platform ◽  
The Family ◽  
Healthy Dogs

Abstract OBJECTIVE To investigate the mycobiome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS 51 dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The whole maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the internal transcribed spacer 2 region with a commercial sequencing platform. RESULTS Fungi were detected in all samples, with a total of 320 fungal species from 135 families detected in the data set. No single fungal species was found in all samples. The 3 most frequently found fungal species were Cladosporium sp (46/51 samples), Malassezia restricta (44/51 samples), and Malassezia arunalokei (36/51 samples). Certain fungi, specifically those of the family Didymellaceae, the family Irpicaceae, and the order Pleosporales, were significantly associated with different stages of periodontitis. Mycobial analysis indicated that Cladosporium sp could be considered part of the core oral cavity mycobiome. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that fungi are present in the oral cavity of dogs and are characterized by substantial species diversity, with different fungal communities associated with various stages of periodontal disease. The next-generation DNA sequencing used in the present study revealed substantially more species of fungi than previous culture-based studies.

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