Journal of Animal Breeding and Genomics (J Anim Breed Genom)
Yu-Ju Lee1,*, Jae-Bong Lee2,*, Kyu-Sang Lim1, Bong-Ki Kim1, Ji-Hyuk Kim1, and Hee-Bok Park1,†
1Department of Animal Resources Science, Kongju National University, Yesan 32439, Korea
2Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea
Correspondence to Hee-Bok Park, E-mail: heebokpark@kongju.ac.kr
†These authors contributed equally to this work.
Volume 7, Number 1, Pages 1-8, March 2023.
Journal of Animal Breeding and Genomics 2023, 7(1), 1-8. https://doi.org/10.12972/jabng.20230001
Received on 07 December, 2022, Revised on 24 March, 2023, Accepted on 28 March, 2023, Published on 31 March, 2023.
Copyright © 2023 Korean Society of Animal Breeding and Genetics.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0).
Nucleotide sequences of DNA contain information about the genetic characteristics of organisms, and in particular, single nucleotide polymorphism (SNP) that shows a difference of one nucleotide sequence in DNA may also affect phenotypic variations. Therefore, it is necessary to precisely read the nucleotide sequence information for the improvement of economically important traits in domestic animals. Sanger sequencing, one of the DNA sequencing methods, is widely used for the verification of genome-wide association study results and the analysis of DNA sequences from small- to medium-scale experiments. Several programs have been developed to analyze such sequencing results, of which STADEN package (https://staden.sourceforge.net), one of the open-source programs, is a useful program with a great cost advantage compared to other commercialized programs that require a license fee. Through the Pregap4 and Gap4 programs installed in the STADEN package, sequence assembly and editing analysis with user-provided settings can be conducted to detect SNPs. The nucleotide sequence results of the STADEN package can be used for follow-up bioinformatic analyses such as database query or phylogenetic analysis.
DNA sequence, Sanger sequencing, STADEN package, Pregap4, Gap4, SNP
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