Related Experiment Video
Updated: Jun 26, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Next generation tools for the annotation of human SNPs
1Biomedical Engineering Department and Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 212218, USA. karchin@jhu.edu
Briefings in Bioinformatics
|February 3, 2009
Summary
Computational biology aids in identifying functional single nucleotide polymorphisms (SNPs) for drug targets. Current webservers offer varied, complex results, necessitating improvements for medical geneticists and molecular biologists.
Area of Science:
- Computational Biology
- Genetics
- Bioinformatics
Background:
- Computational biology is crucial for identifying functional single nucleotide polymorphisms (SNPs) from large genotyping studies.
- Medical genetics and molecular biology increasingly rely on computational methods to prioritize SNPs from association studies.
Purpose of the Study:
- To assess the utility of current web-based computational biology tools for SNP analysis.
- To propose improvements for future webservers to better serve medical geneticists and molecular biologists.
Main Methods:
- Evaluation of existing webserver functionalities for SNP prioritization.
- Analysis of user-friendliness and data accuracy of current tools.
Main Results:
- Current webservers provide conflicting predictions and often require bioinformatics expertise.
- Many tools are biased towards non-synonymous SNPs and may use outdated data sources.
Conclusions:
- There is a need for improved webserver design in computational biology for SNP analysis.
- Next-generation webservers should offer clearer, more accurate, and up-to-date results for medical researchers.
Related Concept Videos
01:05Single Nucleotide Polymorphisms-SNPs
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,...
03:36Genome Annotation and Assembly
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.
02:26Comparing Copy Number Variations and SNPs
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%...
03:00Next-generation Sequencing
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.