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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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2017-09-01
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| Series: | Journal of Microbiology & Biology Education |
| Online Access: | https://journals.asm.org/doi/10.1128/jmbe.v18i2.1295 |
| _version_ | 1818836713086124032 |
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| author | Paul A. Jensen |
| author_facet | Paul A. Jensen |
| author_sort | Paul A. Jensen |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T03:10:58Z |
| format | Article |
| id | doaj.art-67876334c0b845b291db94ef1092b262 |
| institution | Directory Open Access Journal |
| issn | 1935-7877 1935-7885 |
| language | English |
| last_indexed | 2024-12-19T03:10:58Z |
| publishDate | 2017-09-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | Journal of Microbiology & Biology Education |
| spelling | doaj.art-67876334c0b845b291db94ef1092b2622022-12-21T20:38:01ZengAmerican Society for MicrobiologyJournal of Microbiology & Biology Education1935-78771935-78852017-09-0118210.1128/jmbe.v18i2.1295Hands-On Assembly of DNA Sequencing Reads as a Gateway to BioinformaticsPaul A. Jensen0Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801The 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.https://journals.asm.org/doi/10.1128/jmbe.v18i2.1295 |
| spellingShingle | Paul A. Jensen Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics Journal of Microbiology & Biology Education |
| title | 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_short | 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 |
| url | https://journals.asm.org/doi/10.1128/jmbe.v18i2.1295 |
| work_keys_str_mv | AT paulajensen handsonassemblyofdnasequencingreadsasagatewaytobioinformatics |