A Small-Group Activity Introducing the Use and Interpretation of BLAST

As biological sequence data are generated at an ever increasing rate, the role of bioinformatics in biological research also grows. Students must be trained to complete and interpret bioinformatic searches to enable them to effectively utilize the trove of sequence data available. A key bioinformati...

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Autores principales:	Peter D. Newell, Ashwana D. Fricker, Constance Armanda Roco, Pete Chandrangsu, Susan M. Merkel
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Special aspects of education LC8-6691 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0372e8d9a5c043af8b1ab194f8617aa2
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spelling	oai:doaj.org-article:0372e8d9a5c043af8b1ab194f8617aa22021-11-15T15:18:40ZA Small-Group Activity Introducing the Use and Interpretation of BLAST10.1128/jmbe.v14i2.6371935-78851935-7877https://doaj.org/article/0372e8d9a5c043af8b1ab194f8617aa22013-01-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/jmbe.v14i2.637https://doaj.org/toc/1935-7877https://doaj.org/toc/1935-7885As biological sequence data are generated at an ever increasing rate, the role of bioinformatics in biological research also grows. Students must be trained to complete and interpret bioinformatic searches to enable them to effectively utilize the trove of sequence data available. A key bioinformatic tool for sequence comparison and genome database searching is BLAST (Basic Local Alignment Search Tool). BLAST identifies sequences in a database that are similar to the entered query sequence, and ranks them based on the length and quality of the alignment. Our goal was to introduce sophomore and junior level undergraduate students to the basic functions and uses of BLAST with a small group activity lasting a single class period. The activity provides students an opportunity to perform a BLAST search, interpret the data output, and use the data to make inferences about bacterial cell envelope structure. The activity consists of two parts. Part 1 is a handout to be completed prior to class, complete with video tutorial, that reviews cell envelope structure, introduces key terms, and allows students to familiarize themselves with the mechanics of a BLAST search. Part 2 consists of a hands-on, web-based small group activity to be completed during the class period. Evaluation of the activity through student performance assessments suggests that students who complete the activity can better interpret the BLAST output parameters % query coverage and % max identity. While the topic of the activity is bacterial cell wall structure, it could be adapted to address other biological concepts.Peter D. NewellAshwana D. FrickerConstance Armanda RocoPete ChandrangsuSusan M. MerkelAmerican Society for MicrobiologyarticleSpecial aspects of educationLC8-6691Biology (General)QH301-705.5ENJournal of Microbiology & Biology Education, Vol 14, Iss 2, Pp 238-243 (2013)
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 Peter D. Newell Ashwana D. Fricker Constance Armanda Roco Pete Chandrangsu Susan M. Merkel A Small-Group Activity Introducing the Use and Interpretation of BLAST
description	As biological sequence data are generated at an ever increasing rate, the role of bioinformatics in biological research also grows. Students must be trained to complete and interpret bioinformatic searches to enable them to effectively utilize the trove of sequence data available. A key bioinformatic tool for sequence comparison and genome database searching is BLAST (Basic Local Alignment Search Tool). BLAST identifies sequences in a database that are similar to the entered query sequence, and ranks them based on the length and quality of the alignment. Our goal was to introduce sophomore and junior level undergraduate students to the basic functions and uses of BLAST with a small group activity lasting a single class period. The activity provides students an opportunity to perform a BLAST search, interpret the data output, and use the data to make inferences about bacterial cell envelope structure. The activity consists of two parts. Part 1 is a handout to be completed prior to class, complete with video tutorial, that reviews cell envelope structure, introduces key terms, and allows students to familiarize themselves with the mechanics of a BLAST search. Part 2 consists of a hands-on, web-based small group activity to be completed during the class period. Evaluation of the activity through student performance assessments suggests that students who complete the activity can better interpret the BLAST output parameters % query coverage and % max identity. While the topic of the activity is bacterial cell wall structure, it could be adapted to address other biological concepts.
format	article
author	Peter D. Newell Ashwana D. Fricker Constance Armanda Roco Pete Chandrangsu Susan M. Merkel
author_facet	Peter D. Newell Ashwana D. Fricker Constance Armanda Roco Pete Chandrangsu Susan M. Merkel
author_sort	Peter D. Newell
title	A Small-Group Activity Introducing the Use and Interpretation of BLAST
title_short	A Small-Group Activity Introducing the Use and Interpretation of BLAST
title_full	A Small-Group Activity Introducing the Use and Interpretation of BLAST
title_fullStr	A Small-Group Activity Introducing the Use and Interpretation of BLAST
title_full_unstemmed	A Small-Group Activity Introducing the Use and Interpretation of BLAST
title_sort	small-group activity introducing the use and interpretation of blast
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/0372e8d9a5c043af8b1ab194f8617aa2
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A Small-Group Activity Introducing the Use and Interpretation of BLAST

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