DNA Barcoding: Bioinformatics Workflows for Beginners

John James Wilson; Kong-Wah Sing; Narong Jaturas

doi:10.1016/B978-0-12-809633-8.20468-8

DNA Barcoding: Bioinformatics Workflows for Beginners

John James Wilson, Kong-Wah Sing, Narong Jaturas

Cyfadran Cyfrifiadureg, Peirianneg a Gwyddoniaeth

Allbwn ymchwil: Pennod mewn Llyfr/Adroddiad/Trafodion Cynhadledd › Pennod › adolygiad gan gymheiriaid

Crynodeb

DNA barcoding is increasingly used to obtain taxonomic information about unidentified organisms. DNA barcoding involves sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, “DNA barcodes,” from taxonomically unknown specimens and performing comparisons with a library of DNA barcodes of known taxonomy. In this article, we provide beginners with step-by-step instructions for (1) converting raw DNA sequences into clean DNA barcodes (sequence editing, sequence alignment), and (2) commonly used tools for DNA barcode comparisons (to assign taxonomic names to DNA barcodes, and to cluster DNA barcodes into Operational Taxonomic Units).

Iaith wreiddiol	Saesneg
Teitl	Reference Module in Life Sciences
Golygyddion	Bernard D. Roitberg
Cyhoeddwr	Elsevier
Nifer y tudalennau	11
ISBN (Electronig)	978-0-12-809633-8
Dynodwyr Gwrthrych Digidol (DOIs)	https://doi.org/10.1016/B978-0-12-809633-8.20468-8
Statws	Cyhoeddwyd - 15 Maw 2018

Mynediad at Ddogfen

10.1016/B978-0-12-809633-8.20468-8Trwydded: CC BY-NC-ND

Dyfynnu hyn

@inbook{7dd9b9d46c8e44978d2e5f5fa44d4063,

title = "DNA Barcoding: Bioinformatics Workflows for Beginners",

abstract = "DNA barcoding is increasingly used to obtain taxonomic information about unidentified organisms. DNA barcoding involves sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, “DNA barcodes,” from taxonomically unknown specimens and performing comparisons with a library of DNA barcodes of known taxonomy. In this article, we provide beginners with step-by-step instructions for (1) converting raw DNA sequences into clean DNA barcodes (sequence editing, sequence alignment), and (2) commonly used tools for DNA barcode comparisons (to assign taxonomic names to DNA barcodes, and to cluster DNA barcodes into Operational Taxonomic Units).",

keywords = "Automatic barcode gap discovery, Barcode of life datasystems , BioEdit, BLAST, CodonCode aligner, FASTA, Neighbor-joining, Operational taxonomic units, Species identification, Taxonomy",

author = "Wilson, {John James} and Kong-Wah Sing and Narong Jaturas",

year = "2018",

month = mar,

day = "15",

doi = "10.1016/B978-0-12-809633-8.20468-8",

language = "English",

editor = "Roitberg, {Bernard D.}",

booktitle = "Reference Module in Life Sciences",

publisher = "Elsevier",

address = "United Kingdom",

}

TY - CHAP

T1 - DNA Barcoding: Bioinformatics Workflows for Beginners

AU - Wilson, John James

AU - Sing, Kong-Wah

AU - Jaturas, Narong

PY - 2018/3/15

Y1 - 2018/3/15

N2 - DNA barcoding is increasingly used to obtain taxonomic information about unidentified organisms. DNA barcoding involves sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, “DNA barcodes,” from taxonomically unknown specimens and performing comparisons with a library of DNA barcodes of known taxonomy. In this article, we provide beginners with step-by-step instructions for (1) converting raw DNA sequences into clean DNA barcodes (sequence editing, sequence alignment), and (2) commonly used tools for DNA barcode comparisons (to assign taxonomic names to DNA barcodes, and to cluster DNA barcodes into Operational Taxonomic Units).

AB - DNA barcoding is increasingly used to obtain taxonomic information about unidentified organisms. DNA barcoding involves sequencing a short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene, “DNA barcodes,” from taxonomically unknown specimens and performing comparisons with a library of DNA barcodes of known taxonomy. In this article, we provide beginners with step-by-step instructions for (1) converting raw DNA sequences into clean DNA barcodes (sequence editing, sequence alignment), and (2) commonly used tools for DNA barcode comparisons (to assign taxonomic names to DNA barcodes, and to cluster DNA barcodes into Operational Taxonomic Units).

KW - Automatic barcode gap discovery

KW - Barcode of life datasystems

KW - BioEdit

KW - BLAST

KW - CodonCode aligner

KW - FASTA

KW - Neighbor-joining

KW - Operational taxonomic units

KW - Species identification

KW - Taxonomy

U2 - 10.1016/B978-0-12-809633-8.20468-8

DO - 10.1016/B978-0-12-809633-8.20468-8

M3 - Chapter

BT - Reference Module in Life Sciences

A2 - Roitberg, Bernard D.

PB - Elsevier

ER -

DNA Barcoding: Bioinformatics Workflows for Beginners

Crynodeb

Mynediad at Ddogfen

Ôl bys

Dyfynnu hyn