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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...
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...
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.
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...

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Related Experiment Video

Updated: May 23, 2026

DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition
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DNAzyme 10-23 - Based Nanomachines for Nucleic Acid Recognition

Published on: February 9, 2024

New encoded single-indicator sequences based on physico-chemical parameters for efficient exon identification.

J K Meher1, P K Meher, G N Dash

  • 1Department of Computer Science and Engineering, Vikash College of Engineering for Women, Vikash Enclave, Bargarh, Odisha, India. jk_meher@yahoo.co.in

International Journal of Bioinformatics Research and Applications
|March 28, 2012
PubMed
Summary

This study introduces new methods for gene identification by converting DNA sequences into numerical signals. These novel approaches improve the accuracy of distinguishing coding DNA (exons) from non-coding DNA (introns).

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Area of Science:

  • Genomic Signal Processing
  • Bioinformatics
  • Computational Biology

Background:

  • Gene identification relies on distinguishing coding (exons) from non-coding (introns) DNA.
  • Existing methods analyze numerical sequences derived from DNA for period-3 peaks.
  • Exons exhibit period-3 peaks, while introns typically lack them.

Purpose of the Study:

  • To develop novel encoding schemes for generating single-indicator DNA sequences.
  • To enhance the accuracy of gene identification using physico-chemical properties.
  • To improve the discrimination between exons and introns.

Main Methods:

  • Converting DNA character strings into numerical sequences.
  • Developing new single-indicator sequence generation methods based on hydration energy and dipole moments.
  • Analyzing sequences for period-3 peaks to identify coding regions.

Main Results:

  • The proposed methods generate sequences with high peaks at exon locations.
  • False exon identification (introns with high peaks) is effectively suppressed.
  • High discriminating factor, sensitivity, and specificity were achieved.

Conclusions:

  • Physico-chemical properties offer a robust basis for DNA sequence encoding.
  • The novel methods significantly improve exon-intron discrimination in gene identification.
  • These approaches enhance the reliability of genomic signal processing for gene discovery.