SNPMeta: SNP annotation and SNP metadata collection without a reference genome
Thomas J Y Kono1, Kiran Seth, Jesse A Poland
1Department of Agronomy & Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA.
Molecular Ecology Resources
|November 19, 2013
Summary
SNPMeta annotates single nucleotide polymorphisms (SNPs) in species lacking a reference genome by comparing sequences to GenBank. This tool aids genetic research in non-model organisms, providing accurate SNP annotations.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Single nucleotide polymorphism (SNP) discovery is accelerating due to increased resequencing data.
- SNP annotation is crucial but challenging, especially in species without a reference genome.
- Current annotation methods rely on reference genomes or manual curation, limiting applicability.
Purpose of the Study:
- To present SNPMeta, a novel bioinformatics tool for SNP annotation.
- To enable SNP annotation in species lacking a reference genome.
- To facilitate genetic studies in non-model organisms and agriculturally important species.
Main Methods:
- SNPMeta compares SNP sequences against publicly available GenBank databases.
- The tool annotates SNPs from SNP assay designs and genotyping by sequencing (GBS) data.
- It processes contextual sequence information surrounding identified SNPs.
Main Results:
- SNPMeta successfully annotates SNPs by leveraging cDNA and well-annotated gene data.
- The tool demonstrates high concordance with annotations derived from reference genomes.
- SNPs from GBS approaches, which are genome-wide, show lower annotation rates compared to gene-specific SNPs.
Conclusions:
- SNPMeta provides a valuable solution for SNP annotation in species without a reference genome.
- The tool enhances the utility of genetic data for non-model and agriculturally significant species.
- SNPMeta's annotations are reliable and comparable to those obtained using reference genomes.
More Related Videos
09:34Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
36.1K
09:10A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
10.6K
Related Concept Videos
03:36Genome Annotation and Assembly
16.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
16.8K
01:11Genome-wide Association Studies-GWAS
12.7K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
12.7K
01:05Single Nucleotide Polymorphisms-SNPs
14.8K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
14.8K
01:57Sanger Sequencing
801.1K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
801.1K
03:00Next-generation Sequencing
88.0K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
88.0K
02:26Comparing Copy Number Variations and SNPs
11.6K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
11.6K