Mathematical Biology & Bioinformatics | Volume 19 Issue 1 Year 2024

Kipen V.N., Snytkov E.V.

GENIS – methodological approach for in silico genotyping (validation on Sus scrofa sequencing)

Mathematical Biology & Bioinformatics. 2024;19(1):36-51.

doi: 10.17537/2024.19.36.

References

Rabtsava A.A., Tsybovsky I.S., Kotova S.A. Microsatellite markers in the study of polymorphism of the wild boar (Sus scrofa) and domestic pig (Sus scrofa domesticus), inhabiting the territory of the Repablic of Belarus. Molekulyarnaya i prikladnaya genetika. 2018;25:56–65.
Rębała K., Rabtsava A.A., Kotova S.A., Kipen V.N., Zhurina N.V., Gandzha A.I., Tsybovsky I.S. STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus. PLoS One. 2016;11(11):e0166563. doi: 10.1371/journal.pone.0166563
Nosova A.Yu., Kipen V.N., Tsar A.I., Lemesh V.A. Differentiation of hybrid offspring of silver (Hypophthalmichthys molitrix val.) and bighead (H. nobilis rich.) carps based on microsatellite loci analysis. Russian Journal of Genetics. 2020;56(3):317–323. doi: 10.1134/S1022795420030126
Conyers C.M., Allnutt T.R., Hird H.J., Kaye J., Chisholm J. Development of a microsatellite-based method for the differentiation of European wild boar (Sus scrofa scrofa) from domestic pig breeds (Sus scrofa domestica) in food. Journal of Agricultural and Food Chemistry. 2012;60(13):3341–3347. doi: 10.1021/jf205109b
Lorenzini R., Fanelli R., Tancredi F., Siclari A., Garofalo L. Matching STR and SNP genotyping to discriminate between wild boar, domestic pigs and their recent hybrids for forensic purposes. Scientific Reports. 2020;10:3188. doi: 10.1038/s41598-020-59644-6
Koseniuk A., Smołucha G., Gurgul A., Szmatoła T., Oczkowicz M., Radko A. Differentiation of the domestic pig and wild boar using genotyping-by-sequencing. Folia Biologica (Kraków). 2023;71(1):1–11. doi: 10.3409/fb_71-1.01
Koseniuk A., Smołucha G., Natonek-Wiśniewska M., Radko A., Rubiś D. Differentiating Pigs from Wild Boars Based on NR6A1 and MC1R Gene Polymorphisms. Animals (Basel). 2021;11(7):2123. doi: 10.3390/ani11072123
Unipro UGENE. https://ugene.net/ (accessed 16.01.2024).
Genome Analysis Toolkit. https://gatk.broadinstitute.org/hc/en-us (accessed 16.01.2024).
ANNOVAR. https://annovar.openbioinformatics.org/en/latest/ (accessed 16.01.2024).
SnpEff & SnpSift. http://pcingola.github.io/SnpEff/ (accessed 16.01.2024).
Whole genome association analysis toolset. https://zzz.bwh.harvard.edu/plink/ (accessed 16.01.2024).
SNPTEST. https://www.well.ox.ac.uk/~gav/snptest/ (accessed 16.01.2024).
BioSample. https://www.ncbi.nlm.nih.gov/biosample (accessed 16.01.2024).
BioProject. https://www.ncbi.nlm.nih.gov/bioproject (accessed 16.01.2024).
Sequence Read Archive (SRA). https://www.ncbi.nlm.nih.gov/sra (accessed 16.01.2024).
BGISEQ. https://www.bgi.com/global/overview/business-overview?i=3 (accessed 16.01.2024).
Illumina sequencing platforms. https://www.illumina.com/systems/sequencing-platforms.html (accessed 16.01.2024).
Roche Sequencing Solutions. https://diagnostics.roche.com/global/en/about/about-roche-sequencing-solutions.html (accessed 16.01.2024).
PACBIO SMRT, Sequencing systems. https://www.pacb.com/sequencing-systems/ (accessed 16.01.2024).
OXFORD NANOPORE. https://nanoporetech.com/products (accessed 16.01.2024).
Kipen V.N., Snytkov E.V., Mikhailova M.E., Sheyko R.I. Breed differentiation of domestic pigs using SNP – extended bioinformatical analysis. Doklady Natsional’noi akademii nauk Belarusi (Doklady of the National Academy of Sciences of Belarus). 2022;66(3):301–309 (in Russ.). doi: 10.29235/1561-8323-2022-66-3-301-309
Axiom™ Porcine Genotyping Array. https://www.thermofisher.com/order/catalog/product/550588 (accessed 16.01.2024).
Oligo Calc: Oligonucleotide Properties Calculator. http://biotools.nubic.northwestern.edu/OligoCalc.html (accessed 16.01.2024).
Kipen V.N., Mikhailova M.E., Snytkov E.V., Romanishko E.L., Ivanova E.V., Sheyko R.I. Bioinformatic analysis of genomes of commercial breeds of domestic pigs for identification of breed-specific SNPs. Vestsі Natsyyanal’nay akademіі navuk Belarusі. Seryya agrarnykh navuk (Proceedings of the National Academy of Sciences of Belarus. Agrarian series). 2021;59(4):464–476 (in Russ.). doi: 10.29235/1817-7204-2021-59-4-464-476
Kipen V.N., Ivanova E.V., Snytkov E.V., Verchuk A.N. Analysis of HEPH Gene Polymorphism on the X Chromosome for Identification of Wild Boar and Domestic Pig. Russian Journal of Genetics. 2020;56(9):1099–1108. doi: 10.1134/S1022795420080062
Kipen V.N., Rabcava A.O., Kotava S.A., Zhurina N.V., Handza A.I., Tsybovsky I.S. Polymorphism analysis of MC1R and NR6A1 genes to evaluate the level of introgression of domestic swine (Sus scrofa domesticus) genes in wild boar (Sus scrofa scrofa) population. Molekulyarnaya i prikladnaya genetika. 2019;26:83–95 (in Russ.).