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Related Concept Videos

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%...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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...
Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...

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Related Experiment Video

Updated: Jun 15, 2026

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

Calling SNPs without a reference sequence.

Aakrosh Ratan1, Yu Zhang, Vanessa M Hayes

  • 1Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA. ratan@bx.psu.edu.

BMC Bioinformatics
|March 17, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces DIAL, a computational pipeline for identifying genetic differences between individuals without a reference genome. This method aids in surveying genetic diversity, especially for endangered species lacking genomic resources.

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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
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Rare Event Detection Using Error-corrected DNA and RNA Sequencing

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Last Updated: Jun 15, 2026

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

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Population Genetics

Background:

  • Next-generation sequencing (NGS) is crucial for identifying genetic variations.
  • Current methods primarily rely on aligning short reads to a reference genome.
  • A significant limitation exists for species lacking available reference genomes.

Purpose of the Study:

  • To develop a computational pipeline for identifying genetic differences without a reference genome.
  • To enable genetic variation analysis in species lacking genomic resources.
  • To facilitate the study of genetic diversity in endangered species.

Main Methods:

  • Developed DIAL (De novo Identification of Alleles), a computational pipeline.
  • DIAL identifies single-base substitutions and small insertions/deletions.
  • Evaluated using existing sequencing data from human and orangutan genomes.

Main Results:

  • DIAL effectively identifies nucleotide differences without a reference genome.
  • The method is robust even with insufficient depth of coverage for de novo assembly.
  • Demonstrated utility in identifying variations in transcriptome sequences.

Conclusions:

  • DIAL enables genetic variation analysis in species lacking reference genomes.
  • This tool can survey genetic diversity in endangered species.
  • Identified sequence differences can inform the design of genotyping arrays for species management.