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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-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.
Single Nucleotide Polymorphisms-SNPs01:05

Single 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,...
Comparing Copy Number Variations and SNPs02:26

Comparing 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%...
Sanger Sequencing01:57

Sanger Sequencing

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...

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Related Experiment Video

Updated: Jul 10, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

novoSNP3: variant detection and sequence annotation in resequencing projects.

Peter De Rijk, Jurgen Del-Favero

    Methods in Molecular Biology (Clifton, N.J.)
    |November 21, 2007
    PubMed
    Summary

    novoSNP software efficiently identifies genetic variations like single nucleotide polymorphisms and insertion-deletion polymorphisms from DNA resequencing data. This tool aids in managing and analyzing large-scale genetic projects, accelerating variant discovery.

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    Last Updated: Jul 10, 2026

    Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
    09:34

    Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

    Published on: April 4, 2018

    Novel Sequence Discovery by Subtractive Genomics
    09:40

    Novel Sequence Discovery by Subtractive Genomics

    Published on: January 25, 2019

    Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
    14:06

    Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

    Published on: June 23, 2012

    Area of Science:

    • Genomics and Bioinformatics
    • Molecular Biology

    Background:

    • High-throughput sequencing enables genomic analysis but poses data management challenges.
    • Resequencing is crucial for identifying genetic variants, yet analysis bottlenecks hinder large projects.

    Purpose of the Study:

    • To develop a user-friendly software package for efficient discovery of genetic variants.
    • To address the data analysis limitations in large-scale resequencing projects.

    Main Methods:

    • Development of the novoSNP software package.
    • Utilizing high-throughput sequencing data (sequence trace files).
    • Implementation of algorithms for variant discovery and data management.

    Main Results:

    • novoSNP reliably and rapidly discovers single nucleotide polymorphisms and insertion-deletion polymorphisms.
    • The software facilitates database creation, data alignment, variant annotation, and reporting.
    • novoSNP supports both MS Windows and Linux operating systems.

    Conclusions:

    • novoSNP effectively overcomes data analysis bottlenecks in resequencing projects.
    • The software provides a comprehensive solution for variant discovery, annotation, and genotype reporting.
    • novoSNP enhances the efficiency and reliability of genetic variation analysis.