Citation
Kanthaswamy, Sree and Wilson, John-James and Malaivijitnond, Suchinda
(2025)
DNA barcoding: bioinformatics and phylogenetic workflow in R.
In:
Encyclopedia of Bioinformatics and Computational Biology (Second Edition).
Elsevier, pp. 126-147.
ISBN 9780323955034
Abstract
DNA barcoding is used to (i) assign taxonomic identity to unknown organisms and (ii) obtain taxonomic information about cryptic species. It involves sequencing a fragment of mitochondrial COI gene (=DNA barcodes) from specimens and performing comparisons with a library of DNA barcodes of known taxonomy. Here, in an update to the previous edition, we provided step-by-step instructions for using R, an open-source offline platform, to (1) convert sequencing reads into DNA barcodes and (2) analyse the barcodes with phylogenetic trees. We also provided steps of using BOLD, an online COI database, to perform the assignment of taxonomic identity.
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Official URL or Download Paper: https://linkinghub.elsevier.com/retrieve/pii/B9780...
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Additional Metadata
| Item Type: | Book Section |
|---|---|
| Divisions: | Faculty of Forestry |
| DOI Number: | https://doi.org/10.1016/B978-0-323-95502-7.00243-8 |
| Publisher: | Elsevier |
| Keywords: | DNA barcoding; Bioinformatics; Phylogenetics; R; COI gene; Mitochondrial DNA; BOLD database; Taxonomic identification; Cryptic species; Phylogenetic trees; Sequence analysis; Open-source software |
| Depositing User: | Dr. Voon Ching Lim |
| Date Deposited: | 07 Apr 2025 02:11 |
| Last Modified: | 07 Apr 2025 02:11 |
| Altmetrics: | http://www.altmetric.com/details.php?domain=psasir.upm.edu.my&doi=10.1016/B978-0-323-95502-7.00243-8 |
| URI: | http://psasir.upm.edu.my/id/eprint/116399 |
| Statistic Details: | View Download Statistic |
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