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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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,...
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Genome Annotation and Assembly03:36

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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.
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Comparing Copy Number Variations and SNPs02:26

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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.
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Nucleic Acid Structure01:25

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
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Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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...
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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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Identification and Classification of Position-specific GABAA Receptor Subunit Missense Variants for Their Role In Hippocampal Pyramidal Neurons
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StructMAn: annotation of single-nucleotide polymorphisms in the structural context.

Alexander Gress1, Vasily Ramensky2, Joachim Büch3

  • 1Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany Graduate School of Computer Science, Saarland University, Campus E1 3, 66123 Saarbrücken, Germany.

Nucleic Acids Research
|May 7, 2016
PubMed
Summary
This summary is machine-generated.

StructMAn annotates non-synonymous single nucleotide variants (nsSNVs) using 3D protein structures. This tool provides crucial structural context for genetic variations, aiding phenotype interpretation.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Structural Biology

Background:

  • Next-generation sequencing generates vast genetic data, including variations.
  • Non-synonymous single nucleotide variants (nsSNVs) significantly alter protein sequences and can impact phenotypes.
  • Existing tools lack comprehensive structural context for nsSNVs.

Purpose of the Study:

  • To develop StructMAn, a web-based tool for annotating nsSNVs within their structural context.
  • To analyze the spatial positioning of nsSNVs relative to protein structures, nucleic acids, and ligands.
  • To enhance the interpretation of genetic variations by providing structural insights.

Main Methods:

  • StructMAn utilizes experimentally determined 3D protein structures.
  • It incorporates structures of homologous proteins with detectable sequence identity.
  • The tool analyzes the spatial location of nsSNVs within protein structures.

Main Results:

  • StructMAn provides structural context for approximately 20% of human nsSNVs and up to 60% in disease-related genes.
  • For bacterial samples, it offers context for around 35% of nsSNVs.
  • Users can visualize and inspect each nsSNV within its 3D protein structure or complex.

Conclusions:

  • StructMAn significantly improves the structural annotation of nsSNVs across various organisms.
  • The tool aids in understanding the phenotypic impact of genetic variations by providing spatial context.
  • StructMAn is accessible via a web server for broad research application.