Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics

The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly proces...

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Autor principal:	Paul A. Jensen
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Special aspects of education LC8-6691 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/67876334c0b845b291db94ef1092b262
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spelling	oai:doaj.org-article:67876334c0b845b291db94ef1092b2622021-11-15T15:04:06ZHands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics10.1128/jmbe.v18i2.12951935-78851935-7877https://doaj.org/article/67876334c0b845b291db94ef1092b2622017-09-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/jmbe.v18i2.1295https://doaj.org/toc/1935-7877https://doaj.org/toc/1935-7885The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly process using short DNA sequences printed on paper. Topics highlighted during the lesson include overlap identification, reference sequences, and the challenges arising from sequencing errors, low-frequency mutations, and repetitive regions. Sample materials provide reads and solutions for assembling clinically relevant regions of the S. gordonii penicillin binding protein and the human HTT gene. An online tool allows instructors to generate custom read sets from other DNA sequences.Paul A. JensenAmerican Society for MicrobiologyarticleSpecial aspects of educationLC8-6691Biology (General)QH301-705.5ENJournal of Microbiology & Biology Education, Vol 18, Iss 2 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Special aspects of education LC8-6691 Biology (General) QH301-705.5
spellingShingle	Special aspects of education LC8-6691 Biology (General) QH301-705.5 Paul A. Jensen Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics
description	The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly process using short DNA sequences printed on paper. Topics highlighted during the lesson include overlap identification, reference sequences, and the challenges arising from sequencing errors, low-frequency mutations, and repetitive regions. Sample materials provide reads and solutions for assembling clinically relevant regions of the S. gordonii penicillin binding protein and the human HTT gene. An online tool allows instructors to generate custom read sets from other DNA sequences.
format	article
author	Paul A. Jensen
author_facet	Paul A. Jensen
author_sort	Paul A. Jensen
title	Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics
title_short	Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics
title_full	Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics
title_fullStr	Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics
title_full_unstemmed	Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics
title_sort	hands-on assembly of dna sequencing reads as a gateway to bioinformatics
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/67876334c0b845b291db94ef1092b262
work_keys_str_mv	AT paulajensen handsonassemblyofdnasequencingreadsasagatewaytobioinformatics
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Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics

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