Illuminating the Black Box of Genome Sequence Assembly: A Free Online Tool to Introduce Students to Bioinformatics

被引：1

作者：

Taylor, D. Leland ^{[1
]}

Campbell, A. Malcolm ^{[2
]}

Heyer, Laurie J. ^{[2
]}

机构：

[1] Davidson Coll, Ctr Interdisciplinary Studies, Davidson, NC 28035 USA

[2] Davidson Coll, Davidson, NC 28035 USA

来源：

AMERICAN BIOLOGY TEACHER | 2013年 / 75卷 / 08期

关键词：

Genome assembly; bioinformatics; computational biology; teaching tool;

D O I：

10.1525/abt.2013.75.8.9

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Next-generation sequencing technologies have greatly reduced the cost of sequencing genomes. With the current sequencing technology, a genome is broken into fragments and sequenced, producing millions of "reads." A computer algorithm pieces these reads together in the genome assembly process. PHAST is a set of online modules (http://gcat. davidson. edu/phast) designed to teach advanced high school and college students the genome assembly process. PHAST allows users to assemble phage genomes in real time and includes tutorials detailing the complexities of genome assembly. With PHAST, students learn concepts behind genome assembly and understand how mathematics solves biological problems such as genome assembly.

引用

页码：572 / 577

页数：6

共 11 条

[1] GATB: Genome Assembly & Analysis Tool Box
Drezen, Erwan
Rizk, Guillaume
Chikhi, Rayan
Deltel, Charles
Lemaitre, Claire
Peterlongo, Pierre
Lavenier, Dominique
BIOINFORMATICS, 2014, 30 (20) : 2959 - 2961
[2] CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects
Frangeul, L
Glaser, P
Rusniok, C
Buchrieser, C
Duchaud, E
Dehoux, P
Kunst, F
BIOINFORMATICS, 2004, 20 (05) : 790 - U758
[3] Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence
Iida, Naoko
Yamao, Fumiaki
Nakamura, Yasukazu
Iida, Tetsushi
GENES TO CELLS, 2014, 19 (06) : 517 - 527
[4] Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence
Gongora-Castillo, Elsa
Buell, C. Robin
NATURAL PRODUCT REPORTS, 2013, 30 (04) : 490 - 500
[5] Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence
Huerlimann, Roger
Cowley, Jeff A.
Wade, Nicholas M.
Wang, Yinan
Kasinadhuni, Naga
Chan, Chon-Kit Kenneth
Jabbari, Jafar
Siemering, Kirby
Gordon, Lavinia
Tinning, Matthew
Montenegro, Juan D.
Maes, Gregory E.
Sellars, Melony J.
Coman, Greg J.
McWilliam, Sean
Zenger, Kyall R.
Khatkar, Mehar S.
Raadsma, Herman W.
Donovan, Dallas
Krishna, Gopala
Jerry, Dean R.
G3-GENES GENOMES GENETICS, 2022, 12 (04):
[6] Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data
Ramirez-Gonzalez, Ricardo
Caccamo, Mario
MacLean, Daniel
BIOINFORMATICS, 2011, 27 (19) : 2754 - 2755
[7] Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions
Chad Laing
Cody Buchanan
Eduardo N Taboada
Yongxiang Zhang
Andrew Kropinski
Andre Villegas
James E Thomas
Victor PJ Gannon
BMC Bioinformatics, 11
[8] Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions
Laing, Chad
Buchanan, Cody
Taboada, Eduardo N.
Zhang, Yongxiang
Kropinski, Andrew
Villegas, Andre
Thomas, James E.
Gannon, Victor P. J.
BMC BIOINFORMATICS, 2010, 11
[9] ExpansionHunter: A software tool to detect long repeat expansions from PCR-free whole-genome sequence data
Eberle, M. A.
Dolzhenko, E.
van Vugt, J. J. F. A.
Narzisi, G.
Veldink, J. H.
Bentley, D. A.
EUROPEAN JOURNAL OF HUMAN GENETICS, 2019, 27 : 596 - 597
[10] Nanopore reads spanning the whole genome of arthropod-infecting large dsDNA viruses of the class Naldaviricetes enable assembly-free sequence analysis
Wennmann, Jorg T.
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