VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
| Autor: | Joanna Augustynowicz, Marek Szklarczyk, Wojciech Wesołowski, Beata Domnicz |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0301 basic medicine Heredity Single Nucleotide Polymorphisms Datasets as Topic Artificial Gene Amplification and Extension Polymerase Chain Reaction 01 natural sciences Homozygosity Cleaved amplified polymorphic sequence Biology (General) education.field_of_study Heterozygosity Ecology Software Engineering High-Throughput Nucleotide Sequencing Genomics Genetic Mapping Restriction site Molecular Diagnostic Techniques Computational Theory and Mathematics Modeling and Simulation Engineering and Technology Research Article Genetic Markers Computer and Information Sciences Genotype QH301-705.5 Population Variant Genotypes Computational biology Biology Research and Analysis Methods DNA sequencing Computer Software 03 medical and health sciences Cellular and Molecular Neuroscience Genetics Molecular Biology Techniques education Indel Molecular Biology Alleles Ecology Evolution Behavior and Systematics Biology and Life Sciences Molecular diagnostics Restriction enzyme 030104 developmental biology Genetic Loci Software 010606 plant biology & botany |
| Zdroj: | PLoS Computational Biology, Vol 17, Iss 5, p e1008980 (2021) PLoS Computational Biology |
| ISSN: | 1553-7358 |
| Popis: | Next-generation sequencing (NGS) is a powerful tool for massive detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertions/deletions (indels). For routine screening of numerous samples, these variants are often converted into cleaved amplified polymorphic sequence (CAPS) markers which are based on the presence versus absence of restriction sites within PCR products. Current computational tools for SNP to CAPS conversion are limited and usually infeasible to use for large datasets as those generated with NGS. Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS–a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments. Additionally, the program contains filtration utilities not available in other SNP to CAPS converters–selection of markers with a single polymorphic cut site within a user-specified sequence length, and selection of markers that differentiate up to three user-defined groups of individuals from the analyzed population. Performance of VCF2CAPS was tested on a thoroughly analyzed dataset from a genotyping-by-sequencing (GBS) experiment. A selection of CAPS markers picked by the program was subjected to experimental verification. CAPS markers, also referred to as PCR-RFLPs, belong to basic tools exploited in plant, animal and human genetics. Our new software–VCF2CAPS–fills the gap in the current inventory of genetic software by high-throughput CAPS marker design from next-generation sequencing (NGS) data. The program should be of interest to geneticists involved in molecular diagnostics. In this paper we show a successful exemplary application of VCF2CAPS and we believe that its usefulness is guaranteed by the growing availability of NGS services. |
| Databáze: | OpenAIRE |
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