Analysis of DNA Barcodes Using DNA Subway

Jason Williams; Bruce Nash; Cornel Ghiban; Mohammed Khalfan; Uwe Hilgert; Susan Lauter; Chun-Hua Yang; David Andrew Micklos

doi:10.1007/978-1-0716-3581-0_34

Analysis of DNA Barcodes Using DNA Subway

Methods Mol Biol. 2024:2744:551-560. doi: 10.1007/978-1-0716-3581-0_34.

Authors

Jason Williams¹, Bruce Nash², Cornel Ghiban², Mohammed Khalfan², Uwe Hilgert², Susan Lauter², Chun-Hua Yang², David Andrew Micklos²

Affiliations

¹ Cold Spring Harbor Laboratory DNA Learning Center, Cold Spring Harbor, NY, USA. [email protected].
² Cold Spring Harbor Laboratory DNA Learning Center, Cold Spring Harbor, NY, USA.

PMID: 38683342
DOI: 10.1007/978-1-0716-3581-0_34

Abstract

DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees. High-quality sequences with the required metadata can also be submitted as barcode sequences to NCBI GenBank.

Keywords: BLAST; Bioinformatics; DNA barcoding; DNA sequencing; Multiple sequence alignment; NCBI GenBank; Phylogenetic tree.

MeSH terms

Computational Biology* / methods
DNA / genetics
DNA Barcoding, Taxonomic* / methods
High-Throughput Nucleotide Sequencing / methods
Phylogeny
Sequence Analysis, DNA / methods
Software*
Workflow

Substances

DNA